Diagnosing congenitally missing second premolars (SPs) in early childhood is challenging due to variations in their calcification ages. In this study, we investigated the correlation between calcification grades of SPs and other permanent posterior teeth to aid clinicians in the early diagnosis of congenitally missing SPs. This cohort study retrospectively evaluated 6813 images from 9261 panoramic image records of children aged 42–78 months. The Nolla method was used to score calcification grades of first and SP and first and second permanent molars. Images were divided into 6 subgroups based on age with six-month intervals, and average calcification grades of teeth were analyzed by gender and categorized. The calcification grades of these relevant teeth were separately analyzed, specifically for Grade 0 and Grade 1 for SPs. Gender-based analysis revealed statistically significant differences in the calcification grades of 4 first premolars, 4 permanent first molars, and 2 permanent second molars. However, these differences were not significant for all 4 SPs and teeth numbered 17 and 27 between genders. Generally, Nolla grades were higher in girls compared to boys, except for all 4 SPs and tooth numbered 46. Furthermore, higher Nolla grades were observed in older age groups, which was consistent with expectations. The variability in calcification grades of SPs highlights the importance of understanding the calcification grades of other permanent teeth, which are more clearly visible on radiological images of young children. This knowledge could help clinicians in assessing the dental maturity of pediatric patients and facilitate early diagnosis of congenitally missing teeth.