By the time most people start comparing TMS clinics, they've already been through a lot: two or three antidepressants, maybe more, often a stretch of therapy, and the slow realization that something still isn't working. Then the search results come back with a dozen Bay Area clinics, from San Francisco to San Jose, that all seem to say the same thing.
They aren't the same. Choosing the right TMS therapy clinic in the Bay Area comes down to a handful of checks: how carefully the clinic screens you, which protocol it uses, whether your insurance will pay, whether you can actually get there five days a week, and who looks after you once the last session ends. Below is each check, the questions to put to any clinic on a first call, and a plain account of what we do and don't offer at our Los Altos and San Mateo clinics.
How to choose a TMS clinic: 7 things to check
- Confirm that a psychiatrist reviews your full history before treatment is scheduled.
- Ask which TMS protocol the clinic uses and what it is FDA-cleared to treat.
- Check that the clinic is in-network with your plan and files the prior authorization for you.
- Test the commute at the hour you'd really travel, because a course means dozens of visits.
- Find out who runs each session and how often your symptoms are measured.
- Ask how TMS will fit with your current medication, therapy, and prescriber.
- Ask what the plan is if symptoms come back after the course ends.
The rest of this guide takes those one at a time.
The three kinds of TMS providers in the Bay Area
The Bay Area has more TMS options than most regions, and they sort into three broad groups. Knowing which group a clinic belongs to tells you a lot before you ever call.
TMS-only clinics deliver the treatment and usually rely on your existing psychiatrist for everything else. Integrated practices put TMS inside a broader treatment plan with the same team managing medication, therapy, and follow-up. Neither model is wrong. They just put the work of coordination in different places, and on someone different. We offer both: standalone TMS if you already have a psychiatrist and therapist you want to keep, or TMS as part of full care with our team.
Make sure you're a candidate before you compare clinics
A clinic is only "right" if TMS is a clinically reasonable option for you in the first place. That question gets settled at a screening visit, and a good clinic won't skip it.
What insurers usually look for
Prior authorization is required by most major insurers, and the criteria tend to line up with what clinicians check anyway: a confirmed diagnosis of major depressive disorder (MDD), trials of several antidepressants from different classes without enough improvement, a trial of psychotherapy, and no medical reason to avoid TMS. Plans differ on the details, such as how many medication trials they want documented. At our clinics, getting to a first treatment takes three steps: a psychiatric evaluation, prior authorization, and a mapping visit. We handle the authorization, and its timing depends mostly on your insurer. Ask any clinic how long each step usually takes, since the total wait also depends on gathering past treatment records and booking the mapping visit.
What can rule TMS out
Most of the screening questions are about metal and electrical activity near the head. Metal in or near the head (surgical clips, fragments, some implants) and implanted devices such as cardiac pacemakers or medication pumps can rule TMS out. So can a history of seizures, stroke, brain injury, or neurosurgery, and the team will ask about epilepsy in the family too. Pregnancy calls for an individual assessment with both the psychiatric and obstetric teams. Regular dental fillings are fine.
If a clinic offers to book your first session before anyone has gone through these questions with you, treat that as a reason to keep looking.
Device and protocol: what the labels actually mean
Clinic websites throw around terms like rTMS, theta burst, deep TMS, and SAINT. They describe real differences in how treatment is delivered, and they change both your schedule and what the evidence says.
Standard rTMS, theta burst, and deep TMS
Repetitive TMS (rTMS) is the original form, first cleared by the FDA for depression in 2008. The National Institute of Mental Health describes a standard course as daily sessions five days a week for four to six weeks, and lists side effects that are usually mild: scalp discomfort, tingling of the face or jaw muscles during treatment, and brief headaches or lightheadedness.
Intermittent theta burst stimulation (iTBS) is a newer pattern of pulses that takes about 3 minutes per session instead of 37.5 for a standard 10 Hz session. In a randomized trial at three Canadian university hospitals (Blumberger et al., The Lancet, 2018), iTBS was non-inferior to standard rTMS for treatment-resistant depression. Shorter sessions, similar results. Deep TMS uses a different coil design to reach larger and deeper brain areas.
Ask any clinic which of these it offers and why it would pick one for you. A clear answer is a good sign.
About SAINT and "accelerated" TMS
The Bay Area has a particular connection to accelerated TMS. Stanford neuromodulation therapy (SNT, previously called SAINT) was developed at Stanford: it packs a full course into five days, with several sessions a day, and uses functional MRI to pick each patient's target. In a sham-controlled trial (Cole et al., American Journal of Psychiatry, 2022), the 29 participants analyzed at the interim stage saw a 52.5% average drop in symptoms with active treatment, against 11.1% with sham, four weeks after treatment. The study was small, and the protocol needs imaging and specialized equipment.
That matters when you shop. "Accelerated" on a clinic website can mean many things, from the imaging-guided Stanford protocol to simply more sessions per day. Ask whether the clinic uses MRI-guided targeting and exactly which protocol it delivers. For transparency: we don't offer accelerated TMS. Our Bay Area clinics use the standard daily course.
Run the commute test
This is the check people skip, and it's often the one that decides whether they finish. At our Los Altos and San Mateo clinics, a standard course runs about 36 sessions over six to nine weeks, with appointments Monday through Friday. After the first mapping visit, a typical session takes about 10 minutes, only 3 to 5 of which are the stimulation itself. The visit is short. The trip there is what you're really signing up for, roughly 36 times.
A clinic that looks close on a map can still be a 50-minute drive at the hour you'd need to go. Before you commit, do the drive once at your real appointment time, from wherever you'll actually be that day: home, the office, or school drop-off. Ask the clinic which time slots are open, how much flexibility there is if your week changes, and what happens if you miss a session. At our clinics, TMS sessions typically run between 10 a.m. and 3 p.m., so a midday break from work is usually the easiest fit. If you have to miss a day, call the team and the session is added at the end of the course rather than lost.
One thing works in your favor here. TMS needs no anesthesia or sedation, so you can drive home and head right back to work.
Who runs your sessions, and who talks to your psychiatrist
In most clinics, a trained TMS technician runs the day-to-day sessions, while a psychiatric prescriber sets the treatment plan and reviews how you're responding. Ask who will be in the room, which prescriber is responsible for your plan, and how often your symptoms will be rated on a standard scale. Without regular measurement, nobody can tell whether the course is working until it's over.
Here's how it works with us. Your psychiatric prescriber is there in person for the first mapping visit, where they find the right coil position and strength for you and set your treatment parameters. After that, a trained TMS technician from our care coordination team runs your daily sessions under that prescriber's supervision. You'll keep meeting with your prescriber throughout the course, and we track your symptoms with standard questionnaires such as the PHQ-9 for depression, from the first session to the last, so you both can see whether treatment is working.
Then there's everything else in your care. Most people keep taking their medication and seeing their therapist during TMS, so someone has to coordinate. At a TMS-only clinic, that someone is usually you and your outside prescriber. With us, you can choose. If you already have a psychiatrist or therapist, you can keep them and come to us for TMS alone: the evaluation, mapping, treatment, and psychiatric monitoring during the course. If you want more support, TMS can sit inside a coordinated plan with psychiatrists, therapists, primary care clinicians, health coaches, and peer support specialists on the same team.
Ask what happens after the last session
Results from TMS can last, but not always without help. In a 12-month follow-up of 257 patients from 42 clinical practices (Dunner et al., Journal of Clinical Psychiatry, 2014), 62.5% of those who had responded still met response criteria a year later, while staying on antidepressants with access to more TMS if needed. About 36% of the group had TMS reintroduced at some point during the year.
So ask each clinic what happens if symptoms start to return. Who notices? Who adjusts your medication? Can you come back for more sessions, and how fast? A clinic that only thinks in six-to-nine-week blocks may leave those questions with you.
While you're asking about results, notice how the clinic talks about them. "Response" usually means symptoms dropped by about half, and "remission" means they've largely gone. In one real-world study across 42 practices (Carpenter et al., Depression and Anxiety, 2012), 58% of patients met response criteria, and 37% reached remission, based on clinician ratings. A clinic that walks you through numbers like these, without promising where you'll land, is giving you a realistic picture.
Questions to ask on your first call
Keep this list open when you call:
- Who reviews my psychiatric and medical history, and which prescriber oversees my treatment?
- Which protocol and device do you use, and what is it FDA-cleared for?
- Are you in-network with my plan, and who files the prior authorization?
- What appointment times are open, and what is your missed-session policy?
- How do you measure progress, and what happens if I'm not improving halfway through?
- How will you coordinate with my current prescriber and therapist?
- What is the plan if my symptoms return after the course?
Be wary of any clinic that guarantees results, skips the screening questions, or suggests changing your medication without involving the psychiatrist who prescribes it.
TMS at our Los Altos and San Mateo clinics
At two Bay Area clinics, we offer TMS for adults with major depressive disorder that hasn't responded to medication: our Los Altos clinic on South San Antonio Road and our San Mateo clinic on O'Farrell Street. We don't have a clinic in San Francisco itself, so San Mateo is usually the closer option from the city and the northern Peninsula, and Los Altos from the South Bay.
Both clinics are in-network with Aetna, Anthem Blue Cross Blue Shield, Blue Shield of California, Optum, and Evernorth/Cigna. Sliding-scale pricing is available based on financial need. We don't currently accept Medi-Cal or the Health Plan of San Mateo. Same-day appointments are available for a first visit.
You can come to us for TMS alone and keep your current psychiatrist and therapist, or combine it with the integrated psychiatric care we provide for depression, bipolar disorder, and other complex conditions. If you're working out how to choose the right TMS therapy clinic in the Bay Area, start with a screening conversation: request an evaluation and our team will go through your history, your insurance, and whether TMS makes sense for you, or whether another approach fits better.
Frequently asked questions
What disqualifies you for TMS?
The main exclusions are metal in or near the head (other than dental fillings), implanted devices such as pacemakers or medication pumps, and a history of seizures. A history of stroke, brain injury, or neurosurgery can also rule it out. Pregnancy needs an individual assessment. For insurance purposes, you'll also usually need documented trials of several antidepressants and psychotherapy first.
Does insurance cover TMS therapy in California?
Many commercial plans cover TMS for major depressive disorder that hasn't improved with medication, almost always with prior authorization. Criteria vary by plan, so the clinic should run a benefits check before you start. Our Bay Area clinics are not contracted with Medi-Cal for TMS.
How much does TMS cost without insurance?
It depends on the clinic and the protocol, and a full course involves dozens of sessions, so ask for the total course price, not just the per-session rate. At our clinics, cash pay and sliding-scale pricing are available, and our team can walk you through the cost before you commit.
What are the downsides to TMS?
The biggest one is time: daily weekday visits for six to nine weeks at our clinics. Side effects are usually mild, mostly scalp discomfort and headaches that usually ease after the first week or so. Seizure is the most serious risk, and it's very rare. And TMS doesn't work for everyone, which is why measuring progress during the course matters.
Is there a TMS clinic in San Francisco?
Several providers offer TMS in San Francisco, including UCSF. Amae doesn't have a San Francisco clinic. Our nearest locations are San Mateo, a drive down the Peninsula, and Los Altos.