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Background: The morphology and alignment of the patellofemoral joint are crucial risk factors for patellar instability, and the incidence of acute primary patellar dislocation is the highest in women in their second decade of life. The purpose of the study was to analyze age and gender variations of the patellofemoral joint using magnetic resonance imaging (MRI). Methods: A total of 852 patients aged between 4 and 18 years with a history of knee MRI examinations were screened for eligibility and 663 patients (470 males, 193 females) were included. Patients were divided into groups according to age and sex. The age group was divided into five groups (Group 1, 4–6 years; Group 2, 7–9 years; Group 3, 10–12 years; Group 4, 13–15 years; and Group 5, 16–18 years). Three orthopaedic surgeons measured MRI parameters reflecting the patellofemoral morphology (sulcus angle, lateral trochlear inclination, trochlear facet symmetry, and femoral depth) and alignment (tibial tuberosity–trochlear groove distance, percent sulcus location, and percent tibia tuberosity location). Results: Parameters including tibial tuberosity–trochlear groove distance, sulcus angle, percent tibial tuberosity location, trochlear facet symmetry, and femoral depth showed significant differences between the age groups (p < 0.05). The sulcus angle decreased fin Group 2, and the femoral depth showed an increasing trend with aging in male patients. However, the sulcus angle in females decreased first and then increased in Group 3 as the inflection point. The femoral depth showed an opposite pattern. Conclusions: Patellofemoral morphometry showed age and gender variation. Notably, the sulcus angle and femoral depth were significantly different between males and females and changed according to the development. These findings may reflect the sex difference and peak incidence of the patellar instability risk. Understanding the morphological changes and differences of the patellofemoral joint may facilitate the diagnosis of patellofemoral pathologies.