Breast cancer (BC) is a heavy burden for Indonesian healthcare, but there is still no thorough evaluation for Breast self-examination (BSE) practice as routine BC screening. In this study, we aimed to synthesize the pooled prevalence data of BSE practice, compare BSE practice prevalence between Java Island and non-Java Islands in Indonesia, and identify the determinants that we thought could affect the BSE practice in the Indonesian population. Intensive searches were conducted in Cochrane Library, PubMed, Google Scholar, and SINTA (Indonesian Web of Science and Technology Index) from September 2017–2022. We utilized Review Manager 5.4 for conducting the meta-analysis. We found the overall national prevalence of BSE practice was 43.14% (95% CI: 36.08, 50.20, p < 0.00001). BSE practice in Java Island was higher compared to non-Java Island (44.58% vs. 41.62%). The highest prevalence of BSE practice was found among university students, with a 49.90% prevalence. Good knowledge, good attitude toward BSE, family history of BC, family support, and BC information exposure were all statistically associated with a higher determinant of BSE practice. We concluded that BSE practice in Indonesia is still low, especially in non-Java Islands. Integrative and collaborative programs should be established to promote BSE as routine screening for BC.