Purpose: This study proposes a novel magnetic resonance (MRI)-based classification of cortical tubers (CTs) in tuberous sclerosis complex (TSC) patients that incorporates intralesional calcifications. We evaluated prevalence, temporal evolution, and genotype correlation of intra-tuberal calcifications in pediatric TSC patients, emphasizing susceptibility-weighted imaging (SWI) for detection. Materials and Methods: We retrospectively analyzed MRI scans of 57 unrelated pediatric TSC patients followed between 2014 and 2024 at a tertiary care center. Inclusion criteria included longitudinal imaging on the same 1.5T scanner, with T1w, T2w/FLAIR, and SWI sequences. CTs were classified into four MRI-based categories (A–D), with calcified tubers subdivided into micro-calcified and macro-calcified. Descriptive statistics, binomial tests, and Chi-square analyses were performed. Results: Calcified CTs were more prevalent than cystic ones. At baseline MRI, 63% of patients had calcified tubers (19% of all CTs), increasing to 77% at follow-up MRI (24% of all CTs). Micro-calcifications predominated at baseline MRI evaluation, though a significant proportion progressed to macro-calcifications over time. Calcified CTs always progressed from lower-grade lesions. Cystic tubers were rare (<1%). Longitudinal analysis showed significant variation in CTs with inner calcification count (p = 0.0000023), but not in CTs with cystic components (p = 0.42072). No significant genotype–radiological phenotype association emerged. Conclusions: Intralesional calcifications in CTs are dynamic and detectable with SWI. The inclusion of calcification patterns in CT classification could offer insights that may prove useful for future prognostic and risk-stratification frameworks in pediatric TSC.