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Mother-to-child transmission of HIV (MTCT) accounts for a significant proportion of new HIV infections in Peru. The purpose of this case–control study was to examine maternal and infant factors associated with MTCT in Peru from 2015 to 2016. For each biologically confirmed case infant, we randomly selected four birth year- and birth hospital-matched controls from five hospitals in Lima-Callao. Maternal and infant information were gathered from medical records. Simple conditional logistic regression was utilized to examine possible maternal and infant characteristics associated with MTCT. The rate of MTCT was 6.9% in 2015 and 2.7% in 2016. A total of 63 matched controls were identified for 18 cases. Protective factors included higher number of prenatal visits (odds ratio [OR]: 0.72; 95% confidence interval [CI]: 0.55–0.94, p = 0.012) and having more children (OR: 0.10, 95% CI: 0.01–0.79, p = 0.029). Risk factors included later maternal diagnosis (OR: 1.19; 95% CI: 1.06–1.34; p = 0.001) and greater viral load at the time of maternal diagnosis (OR: 1.05; 95% CI: 1.01–1.10; p = 0.022). Our study highlights the importance of targeting early and continued prenatal care as specific areas to target to prevent gaps in the HIV treatment cascade for pregnant HIV-infected women. These strategies can ensure early screening and initiation of antiretroviral therapy to reduce MTCT rates.