Abstract Background Management of health data and its use for informed-decision making is a challenging health sector aspect in developing countries. Monitoring and evaluation of health interventions for meeting health-related Sustainable Development Goals (SDGs), and Cameroon Health Sector Strategy (HSS) targets is facilitated through evidence-based decision-making and public health action. Thus, a routine health information system (RHIS) producing quality data is imperative. The objective of this study was to assess the RHIS in the health facilities (HFs) in Yaoundé in order to identify gaps and weaknesses and to propose measures for strengthening. Methods A health facility-based cross-sectional descriptive study was carried out in the six health districts (HDs) of Yaoundé; followed by a qualitative aspect consisting of in-depth interviews of key informants at the Regional Health Office. HFs were selected using a stratified sampling method with probability proportional to the size of each HD. Data were collected (one respondent per HF) using the World Health Organization and MEASURE Evaluation RHIS rapid assessment tool. Data were entered into Microsoft Excel 2013 and analyzed with IBM-SPSS version 20. Results A total of 111 HFs were selected for the study. Respondents aged 24–60 years with an average of 38.3 ± 9.3 years; 58 (52.3%) male and 53(47.7%) female. Heads of HFs and persons in charge of statistics/data management were most represented with 45.0% and 21.6% respectively. All the twelve subdomains of the RHIS were adequately functioning at between 7 and 30%. These included Human Resources (7%), Data Analysis (10%), Information and Communication Technology (11%), Standards and System Design (15%), Policies and Planning (15%), Information Dissemination (16%), Data Demand and Use (16%), Management (18%), Data Needs (18%), Data Quality Assurance (20%), Collection and Management of Individual Client Data (26%), Collection, Management, and Reporting of Aggregated Facility Data (30%). Conclusions The level of functioning of subdomains of the RHIS in Yaoundé was low; thus, immediate and district-specific strengthening actions should be implemented if health-related SDGs and HSS targets are to be met. A nation-wide assessment should be carried out in order to understand the determinants of these poor performances and to strengthen the RHIS.
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