The purpose of this pilot randomized controlled trial (RCT) was to assess the efficacy of a new muscle stretching and strengthening protocol for the prevention of work-related musculoskeletal disorders (WMSD) in dental hygiene students. Students attending the 2nd and 3rd year of a Dental Hygiene Degree Course of a University Hospital were randomly allocated into treatment group (muscle stretching and strengthening sessions) and control group (no treatment). Nordic Musculoskeletal Questionnaire (NMQ), quality of life, the intensity of the pain and the Global Perceived Effect (GPE) Scale were assessed at the baseline (T0), after 4 weeks (T1) and after 16 weeks (T2). Of 37 subjects screened for eligibility, 28 patients (aged 28.25 ± 8.89 years) were enrolled and divided into treatment and control groups. The NWQ showed significant between-group differences in the following regions from T0 to T2: neck (p = 0.0003), shoulders (p = 0.0057) and lower back (p = 0.0136). In terms of pain, a significant between-group difference was reported from T2 (p < 0.001). The GPE demonstrated that the average satisfaction related to the performed treatment was 1.4 ± 0.63. The present pilot RCT demonstrated the efficacy of stretching associated with muscle strengthening in decreasing the risk of WMSD, especially for the neck, shoulders and lower back. The potential strength of this model is related to the possibility to perform stretching exercises chairside at work during scheduled breaks, in addition to complementary muscle strengthening sessions at home. Future RCTs are necessary to better investigate the role of this protocol for WMSD prevention.