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Mother-to-child transmission (MTCT) is the predominant way for children to acquire human immunodeficiency virus (HIV) infection worldwide including Ethiopia. Thus, objective of this study was to determine the status of prevention of mother-to-child transmission (PMTCT) services utilization and factors affecting PMTCT utilization in health facilities of Afar region, Ethiopia. A cross-sectional study was conducted from December 2014 to April 2015 taking 347 pregnant women and 22 health care providers. Data were collected using a questioner prepared separately for pregnant women and health care providers involved in PMTCT service delivery. Data were analyzed using SPSS considering P value <0.05 statistical significant. The study indicated that the PMTCT service utilization was 67.7%. The study also showed that there is statistically significant association in using PMTCT service with women education level, monthly income, and residence around PMTCT site. Though not statistically significant, excess waiting time, limited physical access to PMTCT sites, and transportation problem were identified as barriers for PMTCT service utilization by pregnant women. Though knowledge of mothers on MTCT of HIV and PMTCT service utilization in agropostural community of Afar region was promising, there were also different barriers identified hindering PMTCT utilization. Thus, we recommend "Wored" and zonal health office to create awareness on significance of PMTCT service in the community, enhance accessibility of PMTCT sites, provide up-to-date trainings for health care providers, and ensure constant supply for PMTCT service.