Temporomandibular dysfunctions are a heterogeneous group of conditions involving the temporomandibular joints (TMJs) and periarticular musculoskeletal structures. This study aimed to evaluate the effectiveness of a physiotherapy program for TMJ dysfunctions and the relationship with cervical spine. The study design was a non-randomized clinical trial with two parallel treatment groups: 33 subjects in the experimental group that underwent conservative drug treatment and physiotherapy treatment, and 31 subjects in the control group that underwent only conservative drug treatment. The participants were examined at baseline and re-examined after 3 months. In this study there was a higher incidence of female subjects. After 3 months of treatment of the TMJs and cervical spine, pain decreased in both groups (p = 0001). Muscle testing at the cervical spine and temporomandibular level showed a decrease in pain and muscles spasms. The average percentage values of the Neck Disability Index (NDI) and the Jaw Functional Limitation Scale 8 (JFLS 8) decreased significantly in both groups, but especially in the experimental group (p = 0.001). Physiotherapy treatments could maintain the functional state at the temporomandibular and cervical levels, thus contributing to increasing the quality of daily life.