Introduction: Musculoskeletal disorders (MSDs) are a significant occupational health concern worldwide, affecting individuals in various professions, including healthcare practitioners. This study aimed to determine the 12-month prevalence of MSDs and identify associated factors among healthcare practitioners in Ouarzazate, in the southeastern region of Morocco. Methods: A cross-sectional study was conducted, collecting data from 120 participants. The Nordic questionnaire was used to identify MSD prevalence and locations. Results: The overall prevalence of MSDs was found to be 89.2%. Lower back pain was the most common reported site of pain, accounting for 63.3% of cases over the past 12 months. Females had a higher prevalence of MSDs (95.0%) compared to males (77.5%) (p-value = 0.009). Midwives had the highest prevalence (93.8%), followed by physiotherapists (87.5%) and general nurses (84%). Professionals working in the shift work system had a higher prevalence of MSDs (92%). Discussion: This study provides important insights into the prevalence and factors associated with MSDs among healthcare practitioners at the Provincial Hospital Center in Ouarzazate. The results underscore the need for targeted interventions and preventive measures to address the high prevalence of MSDs in this population. Such initiatives can contribute to healthcare professionals' well being and occupational health, ultimately enhancing patient care quality.