Job rotation is defined as workers rotating between tasks with different exposure levels and occupational demands. The aim of the present study was to analyze the risk factors for the development of upper-limb work-related musculoskeletal disorders (UL-WMSDs) in poultry slaughterhouse workers as well as compare the score of the OCRA Checklist in different organizational working conditions. In this cross-sectional study, 118 workers were involved, 68 women (32.3 ± 10.7 years) and 50 men (29.5 ± 10.5 years). Three organizational configurations (“without job rotation”, “with job rotation – tasks >1h” and “with job rotation - tasks <1h”) were evaluated using the OCRA Checklist method, totaling 36 tasks and 28 job rotation schemes composed of 2–3 tasks. The OCRA score of the right upper limbs (17.8 ± 3.2) was significantly higher (p = 0.046) relative to the left upper limbs (16.4 ± 3.6). The median score was significantly lower in the “with job rotation - tasks <1h” condition (18.6) when compared to the “job rotation – tasks >1h” (19.4) (p < 0.001) and the “without job rotation” (19.0) (p = 0.038) conditions. However, there was no significant difference between the condition “with job rotation - tasks >1h” and “without job rotation” (p = 0.155). Thus, job rotations with intervals <1h reduced the risk of developing UL-WMSDs. Job rotations with <1 h intervals in poultry slaughterhouses are recommended along with further studies to verify the effectiveness of rotations with more than two tasks, involving mild or non-repetitive tasks.