Purpose The prognostic role of serum cancer antigen 15-3 (CA15-3) and carcinoembryonic antigen (CEA) in breast cancer remains controversial. In this study, we conducted a meta-analysis to investigate the prognostic value of these two markers in breast cancer patients. Methods After electronic databases were searched, 36 studies (31 including information regarding CA15-3 and 23 including information regarding CEA) with 12,993 subjects were included. Based on the data directly or indirectly from the available studies, the hazard ratios (HRs) and odds ratios (ORs) and their 95% confidence intervals (CIs) were pooled according to higher or lower marker levels. Results Elevated CA15-3 or CEA was statistically significant with poorer DFS and OS in breast cancer (multivariate analysis of OS: HR = 2.03, 95% CI 1.76–2.33 for CA15-3; HR = 1.79, 95% CI 1.46–2.20 for CEA; multivariate analysis of DFS: HR = 1.56, 95% CI 1.06–1.55 for CA15-3; HR = 1.77, 95% CI 1.53–2.04 for CEA). Subgroup analysis showed that CA15-3 or CEA had significant predictive values in primary or metastasis types and different cut-offs and included sample sizes and even the study publication year. Furthermore, elevated CA15-3 was associated with advanced histological grade and younger age, while elevated CEA was related to the non-triple-negative tumor type and older age. These two elevated markers were all associated with a higher tumor burden. Conclusions This meta-analysis showed that elevated serum CA15-3 or CEA was associated with poor DFS and OS in patients with breast cancer, and they should be tested anytime if possible.