Background Accessory nerve shoulder dysfunction is common after neck dissection in oral cancer survivors. This study aimed to investigate the short-term effects of scapular muscle strengthening exercises with motor-control techniques on neck dissection-related shoulder dysfunction in oral cancer survivors before the initiation of radiotherapy. Methods Thirty-eight participants were randomly allocated into the motor-control and regular-exercise groups. Each group received conventional physical therapy and specific scapular muscle strengthening exercises for 1 month immediately after neck dissection. Motor control techniques were integrated with scapular strengthening exercises for the motor-control group. Shoulder pain, active range of motion (AROM) of shoulder abduction, and scapular muscle activities including upper trapezius (UT), middle trapezius (MT), lower trapezius (LT), and serratus anterior (SA) when performing maximal voluntary isometric contraction (MVIC) and scapular muscle exercises were evaluated at baseline and after 1 month of training. Results Both groups reduced shoulder pain and increased muscle activity of maximum voluntary isometric contraction (MVIC) of each muscle after the intervention. Increased AROM of shoulder abduction was only observed in the motor-control group (95% CI 3.80 to 20.51, p = 0.004). Relative to baseline evaluation, muscle activities of UT decreased in the motor-control group when performing shoulder shrug with 1-kg weight (95% CI-33.06 to-1.29, p = 0.034). Moreover, the SA activity decreased in the motor-control group (95% CI-29.73 to