In 2011, the Malawi Ministry of Health introduced option B+, a universal treatment strategy for the prevention of mother-to-child transmission (MTCT) of HIV. Under option B+, all pregnant or breastfeeding women with HIV are eligible for lifelong antiretroviral therapy (ART) regardless of clinical stage or CD4. Routine data from Malawi's prevention of MTCT option B+ programme suggest high uptake of antiretroviral therapy (ART) among pregnant women. Malawi's Ministry of Health led the National Evaluation of Malawi's PMTCT Program to obtain nationally representative data on maternal ART coverage and prevention of MTCT effectiveness. Here we present the early transmission data for infants aged 4–12 weeks and used a multistage cluster design to recruit a nationally representative sample of HIV-exposed infants and their mothers. Between October 16, 2014 and May 17, 2016, we screened for HIV in all mothers attending an under-5 vaccination or outpatient sick-child clinic with infants aged 4–26 weeks. They confirmed HIV exposure in 3542 (10·4%) of 33 980 mother (guardian)–infant pairs with infants aged 4–26 weeks. These data suggest that Malawi's decentralization of ART services has resulted in higher ART coverage and lower early MTCT. However, the uptake of services for HIV-exposed infants remains suboptimal.