Health management information system (HMIS) data are important for guiding the attainment of health targets in low- and middle-income countries. However, the quality of HMIS data is often poor. High-quality information is especially important for populations experiencing high burdens of disease and mortality, such as pregnant women, newborns, and children. The purpose of this study was to assess the quality of maternal and child health (MCH) data collected through the Ethiopian Ministry of Health's HMIS in three districts of Jimma Zone, Oromiya Region, Ethiopia over a 12-month period from July 2014 to June 2015. Considering data quality constructs from the World Health Organization's data quality report card, we appraised the completeness, timeliness, and internal consistency of eight key MCH indicators collected for all the primary health care units (PHCUs) located within three districts of Jimma Zone (Gomma, Kersa and Seka Chekorsa). We further evaluated the agreement between MCH service coverage estimates from the HMIS and estimates obtained from a population-based cross-sectional survey conducted with 3,784 women who were pregnant in the year preceding the survey, using Pearson correlation coefficients, intraclass correlation coefficients (ICC), and Bland-Altman plots. We found that the completeness and timeliness of facility reporting were highest in Gomma (75% and 70%, respectively) and lowest in Kersa (34% and 32%, respectively), and observed very few zero/missing values and moderate/extreme outliers for each MCH indicator. We found that the reporting of MCH indicators improved over time for all PHCUs, however the internal consistency between MCH indicators was low for several PHCUs. We found poor agreement between MCH estimates obtained from the HMIS and the survey, indicating that the HMIS may over-report the coverage of key MCH services, namely, antenatal care, skilled birth attendance and postnatal care. The quality of MCH data within the HMIS at the zonal level in Jimma, Ethiopia, could be improved to inform MCH research and programmatic efforts.