Influenza vaccination rates across the US are low. Because few practices send patient reminders for influenza vaccination, a scalable patient reminder system is needed. To evaluate the effect of patient reminders sent via a health care system's electronic health record patient portal on influenza vaccination rates. This pragmatic, 4-arm randomized clinical trial was performed from October 1, 2018, to March 31, 2019, across the UCLA (University of California, Los Angeles) health care system. A total of 164 205 patients in 52 primary care practices who had used the patient portal within 12 months were included. Patients due for an influenza vaccine were sent a letter via the patient portal of the health care system reminding them about the importance of influenza vaccination, safety of the vaccine, and morbidity associated with influenza. Patients were randomized within primary care practices to 1 of 4 study groups (no reminder [n = 41 070] vs 1 reminder [n = 41 055], 2 reminders [n = 41 046], or 3 reminders [n = 41 034]). The primary outcome was receipt of 1 or more influenza vaccines as documented in the electronic health record, which was supplemented with influenza vaccination data from external sources (eg, pharmacies). Secondary outcomes were influenza vaccination rates among subgroups and influenza vaccinations self-reported by patients in reply to the portal-based query as having been received elsewhere. A total of 164 205 patients (mean [SD] age, 46.2 [19.6] years; 95 779 [58.3%] female) were randomly allocated to 1 of the 4 study arms. In the primary analysis across all ages and not including patient self-reported vaccinations in reply to portal reminders, influenza vaccination rates were 37.5% for those receiving no reminders, 38.0% for those receiving 1 reminder (P = .008 vs no reminder), 38.2% for those receiving 2 reminders (P = .03 vs no reminder), and 38.2% for those receiving 3 reminders (P = .02 vs no reminder). In the secondary analysis not including patient self-reported vaccinations, among adults aged 18 to 64 years (vaccination rates: 32.0% in the control group, 32.8% in the 1-reminder group, 32.8% in the 2-reminder group, and 32.8% in the 3-reminder group; P = .001), male patients (vaccination rates: 37.3% vs 38.3%, 38.6%, and 38.8%; P = .001), non-Hispanic patients (vaccination rates: 37.6% vs 38.2%, 38.3%, and 38.2%; P = .004), and those who were not vaccinated in the prior 2 years (vaccination rates: 15.3% vs 15.9%, 16.3%, and 16.1%; P < .001), vaccination rates were higher in the portal reminder groups than in the control group; the findings in these 3 subgroups mirrored the findings in the entire population. When self-reported vaccinations received elsewhere were included, influenza vaccination rates were 1.4 to 2.9 percentage points higher in the portal reminder groups, with a dose-response effect (0 reminders: 15 537 [37.8%]; 1 reminder: 16 097 [39.2%]; 2 reminders: 16 426 [40.0%]; and 3 reminders: 16 714 [40.7%]; P < .001). Generic patient portal reminders were effective in minimally increasing influenza vaccination rates, but more intensive or more targeted patient motivational strategies appear to be needed. ClinicalTrials.gov Identifier: NCT03666026.