Introduction: Prevalence studies on oral lesions in children are scarce, and none of them was conducted in Jordan. Objectives: To determine the prevalence of oral mucosal lesions among Jordanian children. Materials and Methods: A stratified cluster random sampling technique was used to select a sample of first and sixth-grade school children. Systematic oral examination was performed using natural light, and lesions were diagnosed based on the clinical diagnostic criteria proposed by the WHO. Statistical analysis was performed using Statistical Package for Social Sciences (SPSS) version 20 (SPSS Inc., Chicago, IL, USA), and P < 0.05 was considered statistically significant. Data were analyzed using Chi-squared test or Fisher's exact test where appropriate. Results: The study included 1366 school children (639 [46.8%] males and 727 [53.2%] females) of whom 620 (45.4%) were 6-year-old and 746 (54.6%) were 12-year-old. The prevalence of oral lesions among children was 47.4%, without a significant difference in prevalence between males (46.6%) and females (47%). Prevalence was significantly higher in 12-year-old children (50%) compared to 6-year-old children (44.2%; P = 0.032). The most commonly diagnosed lesions were racial pigmentation (16.8%), fissured tongue (14.6%), and hematoma (5.3%). Discussion: Oral mucosal lesions are common in children in general, with no overall preference to gender, but the prevalence increases significantly with age. General dental practitioners and pediatric dentists should be aware of the common oral mucosal lesions in their communities for optimum diagnosis, management, and possible prevention. Conclusions: Oral lesions are common among Jordanian children and dentists should be aware of their diagnosis and management.