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Abstract Background Although IPTp-SP is a lifesaving World Health Organization (WHO) recommended preventive intervention for pregnant women in malaria-endemic regions, IPTp-SP uptake in the Northern region of Ghana is much lower than the sub-optimal national coverage level. Assessing the extent of health workers’ compliance and its associated factors will generate valuable pointers to be targeted at the program level. The study examined the factors influencing health workers’ compliance with the WHO recommended guidelines for IPTp-SP in the Northern Region. Methods A cross-sectional study among 315 health workers in the Northern region was conducted. Semi-structured questionnaires were used to collect data on health workers’ sociodemographic characteristics, facility-based factors and knowledge level. Data were collected on health workers’ compliance with the recommended practices through covert observations using a checklist. Facility observations were carried out using a checklist. Crude and adjusted logistic regression were used to determine predictors of health workers’ compliance, at a 5% significance level adjusting for clustering. Results Of the 315 health workers studied, the median age was 29 years (26–34 years). Females constituted (80.5%; 252) of the 313 workers. The majority (47.4%;148) of the 312 health workers were midwives. Overall, 56.2% (CI 51.0 – 62.0) were adequately complying with the recommended guidelines. Lower levels of compliance were recorded in health centres 15.6% (5.0 – 33.0) and CHPS compounds 21.2% (11.0 – 35.0). The factors associated with compliance included health workers’ knowledge (aOR = 7.64, 95% CI 4.21 – 13.87, p