(1) Background: Children spend a lot of time within schools. The school setting generally has many ergonomic hazards and reinforced behavior patterns which put children at greater risk of environmental hazards than adults during their critical developmental stages. (2) Objective: The aim of the current study was to investigate the prevalence of musculoskeletal disorders (MSDs) and detect spinal deformities amongst general and technical secondary school students. (3) Methods: A total of 418 students from the second grade of secondary school in Shaquira governorate, Egypt participated in this cross-sectional study. Each student in the study was screened via Nordic Musculoskeletal Questionnaire (NMQ) and had their upper limb posture measured via RULA (Rapid Upper Limb assessment), and the deviation in their thoracic curve was measured using a scoliometer. (4) Results: There was a prevalence of MSDs amongst students as there were 69.7% of general school students and 83.8% of the technical school students suffering from MSDs with a statistically significant difference between both technical and general school students in RULA score and musculoskeletal complaints, whereas there were non-statistical differences in the scoliometer scale in both general and technical education students. (5) Conclusions: Musculoskeletal problems are prevalent among Egyptian secondary school students, with higher prevalence between technical school students. Therefore, preventive measures and strategies are recommended to overcome the future complications of these musculoskeletal disorders.