Online programs may help with weight loss but have not been widely implemented in routine primary care. To compare the effectiveness of a combined intervention, including an online weight management program plus population health management, with the online program only and with usual care. Cluster randomized trial with enrollment from July 19, 2016, through August 10, 2017, at 15 primary care practices in the US. Eligible participants had a scheduled primary care visit and were aged 20 to 70 years, had a body mass index between 27 and less than 40, and had a diagnosis of hypertension or type 2 diabetes. Follow-up ended on May 8, 2019. Participants in the usual care group (n = 326) were mailed general information about weight management. Participants in the online program only group (n = 216) and the combined intervention group (n = 298) were registered for the online program. The participants in the combined intervention group also received weight-related population health management, which included additional support from nonclinical staff who monitored their progress in the online program and conducted periodic outreach. The primary outcome was weight change at 12 months based on measured weights recorded in the electronic health record. Weight change at 18 months was a secondary outcome. Among the 840 participants who enrolled (mean age, 59.3 years [SD, 8.6 years]; 60% female; 76.8% White), 732 (87.1%) had a recorded weight at 12 months and the missing weights for the remaining participants were imputed. There was a significant difference in weight change at 12 months by group with a mean weight change of -1.2 kg (95% CI, -2.1 to -0.3 kg) in the usual care group, -1.9 kg (95% CI, -2.6 to -1.1 kg) in the online program only group, and -3.1 kg (95% CI, -3.7 to -2.5 kg) in the combined intervention group (P < .001). The difference in weight change between the combined intervention group and the usual care group was -1.9 kg (97.5% CI, -2.9 to -0.9 kg; P < .001) and the difference between the combined intervention group and the online program only group was -1.2 kg (95% CI, -2.2 to -0.3 kg; P = .01). At 18 months, the mean weight change was -1.9 kg (95% CI, -2.8 to -1.0 kg) in the usual care group, -1.1 kg (95% CI, -2.0 to -0.3 kg) in the online program only group, and -2.8 kg (95% CI, -3.5 to -2.0 kg) in the combined intervention group (P < .001). Among primary care patients with overweight or obesity and hypertension or type 2 diabetes, combining population health management with an online program resulted in a small but statistically significant greater weight loss at 12 months compared with usual care or the online program only. Further research is needed to understand the generalizability, scalability, and durability of these findings. ClinicalTrials.gov Identifier: NCT02656693.