Breast cancer is a major public health concern, particularly among women, and its treatment remains challenging worldwide. Targeted gene therapy may offer a promising approach to reducing the disease burden and improving clinical outcomes. Hence, this study evaluates the mutation patterns of the APC and MYC genes in benign and malignant breast lesions. Ten formalin-fixed heterogeneous paraffin-embedded tissue blocks—five fibroadenomas and five invasive ductal adenocarcinomas (IDA)—from the pathological archives of Federal Teaching Hospital Ido-Ekiti were subjected to analysis. Nucleic acid extraction was performed using the Dellaporta DNA extraction protocol, followed by amplification using polymerase chain reaction (PCR). The samples were subsequently sequenced using the Applied Biosystems 3130xl Genetic Analyzer sequencer following the manufacturer’s instructions. Genetic analyses were conducted using BioEdit and MEGA 6, and HGVSc, HGVSp, and variant allele frequency (%) were evaluated. Transition single-nucleotide polymorphisms (SNPs) were identified in APC for both fibroadenoma and IDA. Functional mutations in APC include silent and missense mutations in fibroadenoma, whereas IDA displayed only missense mutations. In the MYC gene, SNPs in fibroadenoma included both transversions and transitions, whereas transition and transversion SNPs, as well as insertions/deletions, were observed in IDA. Missense and silent functional mutations of MYC were observed in both fibroadenoma and IDA. Overall, the study demonstrated the presence of missense mutations in both APC and MYC genes in fibroadenoma and IDA.