Abstract Background There is very limited evidence examining serious systemic adverse events (SSAEs) and post-injection endophthalmitis of intravitreal bevacizumab (IVB) and intravitreal ranibizumab (IVR) treatments in Thailand and low- and middle-income countries. Moreover, findings from the existing trials might have limited generalizability to certain populations and rare SSAEs. Objectives This prospective observational study aimed to assess and compare the safety profiles of IVB and IVR in patients with retinal diseases in Thailand. Methods Between 2013 and 2015, 6354 patients eligible for IVB or IVR were recruited from eight hospitals. Main outcomes measures were prevalence and risk of SSAEs, mortality, and endophthalmitis during the 6-month follow-up period. Results In the IVB and IVR groups, 94 and 6% of patients participated, respectively. The rates of outcomes in the IVB group were slightly greater than in the IVR group. All-cause mortality rates in the IVB and IVR groups were 1.10 and 0.53%, respectively. Prevalence rates of endophthalmitis and non-fatal strokes in the IVB group were 0.04% of 16,421 injections and 0.27% of 5975 patients, respectively, whereas none of these events were identified in the IVR group. There were no differences between the two groups in the risks of mortality, arteriothrombotic events (ATE), and non-fatal heart failure (HF). Adjustment for potential confounding factors and selection bias using multivariable models for time-to-event outcomes and propensity scores did not alter the results. Conclusions The rates of SAEs in both groups were low. The IVB and IVR treatments were not associated with significant risks of mortality, ATE, and non-fatal HF. Trial Registration Thai Clinical Trial Registry identifier TCTR20141002001.