Background: This study aims to determine the prevalence of generalized joint hypermobility (GJH) in primary school children in relation to age (6–12 years) and gender. It also aims to ascertain whether musculoskeletal pain (MSP) is associated with GJH among these children. Methods: This cross-sectional study was conducted in five primary schools in Al-Madinah al-Munawarah city. The demographic profile recorded includes age, gender, ethnic group, height, weight, and body mass index. The existence of GJH was assessed by the Beighton score (\ge4 was acknowledged as hypermobility). Prior to physical examinations, the Nordic Musculoskeletal Questionnaire was distributed to the students to assist in detecting symptoms in their neck, back, shoulders, and extremities. Results: The study included 563 students (392 boys, 171 girls; average 10.12 \pm 1.588 years; range 6–12 years). GJH was found in 144 students (25.6%). Out of the total number of participants, the occurrence of GJH in male students was 30.87% versus 13.5% in female students, indicating a significant difference (p = 0.001) by gender. GJH was also more prevalent in the age group of 6–9 years (29.2%) compared to that of 10–12 years (23.7%), with a considerable significant difference of p 0.05. With respect to MSP, 222 (39.4%) of the total number of students reported pain. Pain was found in 31 (21.5%) and 191 (45.6%) of hypermobile students and non-hypermobile students, respectively, with a significant difference of p = 0.029. MSP was also not associated with GJH among these children. Conclusions: The prevalence of GJH in the primary school children in this study was markedly higher than the range revealed in some countries in the region but somewhat within the range reported internationally.