Work-related musculoskeletal disorders (WRMDs) are a cause of productivity loss and disability. Resistance training (RT) and stretching seems to relieve pain, reducing the relative workload via an improvement in range of motion. Sixteen women (age: 48.69 ± 5.88 years old, working career duration as a packager: 22.75 ± 2.18 years) were recruited to participate in a 14-week work-based RT and stretching program. Specific exercise training (SET) targeting all body areas affected by WRMDs was performed after week 6. Physical fitness was measured via the 2 min step test (2MST), the back scratch test and the handgrip test (HG). To evaluate the level of pain in the cervical spine, shoulder, elbow and wrist, the visual analogue scale (VAS) was used. Differences were verified with a t-test. The cervical spine (p = 0.02) and left wrist (p = 0.04) VAS decreased, whereas the HG for both right (p = 0.01) and left (p = 0.01) hands and the 2MST (p = 0.01) improved. Participants with WRMDs affecting the cervical spine reported a 3.72 higher VAS score for the neck at the beginning of the protocol (p = 0.03). The protocol improved the physical fitness of participants but showed a limited effect on WRMD pain. The mean adherence was 86.2%, which indicated that exercise performed in the workplace is well accepted and could be used for pain management.