The aims of this study were to evaluate the longitudinal risk of self-harm and the risk factors for self-harm after bariatric surgery in patients and control subjects without prior self-harm. This observational cohort study was based on prospectively registered data. Patients 18–70 years at time of surgery, body mass index (BMI) > 30 kg/m2, who underwent a primary Roux-en-Y gastric bypass (RYGB) procedure or a primary sleeve gastrectomy between 2007 and 2019 were considered for inclusion. All patients who met the inclusion criteria were matched 1:10 to the general population in Sweden (69 492 patients vs. 694 920 controls). After excluding patients and controls with previous self-harm, a self-harm event occurred in 1408 patients in the surgical group (incidence rate (IR) 3.54/1000 person-years, 95% confidence interval (CI) 3.36–3.73) versus in 3162 patients in the control group (IR 0.81/1000 person-years, 95% CI 0.78–0.84), with a hazard ratio (HR) of 4.38 (95% CI 4.11–4.66, p < .001). Median follow-up time was 6.1 years. Risk factors were younger age, lower BMI, cardiovascular, and chronic obstructive pulmonary disease, all aspects of psychiatric comorbidities (except neuropsychiatric disorder), lower socioeconomic status, RYGB, lower health-related quality of life, lower postoperative weight loss, and not attending postoperative follow-up visits. Self-harm is clearly higher after bariatric surgery than in the general population. A qualitative follow-up may be particularly important for patients at increased risk.