Abstract Background Routine Health Information Systems (RHIS) of low-income countries function below the globally expected standard, characterised by the production and use of poor-quality data, or the non-use of good quality data for informed decision making. This has negatively influenced the health service delivery and uptake. This study focuses on identifying the factors associated with the performance of RHIS of the health facilities (HF) in Yaoundé, so as to guide targeted RHIS strengthening. Methods A HF-based cross-sectional study in the 6 health districts (HDs) of Yaoundé was conducted. HFs were chosen using stratified sampling with probability proportional to size per HD. Data were collected, entered into Microsoft Excel 2013 and analysed with IBM- SPSS version 25. Consistency of the questionnaire was measured using Cronbach’s alpha coefficient. Pearson’s chi-square (and Fisher exact where relevant) tests were used to establish relationships between qualitative variables. Associations were further quantified using unadjusted Odd ratio (OR) for univariable analysis and adjusted odds ratio (aOR) for multivariable analysis with 95% confidence interval (CI). A p-value of less than 0.05 was considered statistically significant. Results Of 111 selected HFs; 16 (14.4%) were public and 95 (85.6%) private. Respondents aged 24–60 years with an average of 38.3 ± 9.3 years; 58 (52.3%) males and 53(47.7%) females. Cronbach’s alpha was 0.96 (95%CI: 0.95–0.98, p
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