Background Bacillus Calmette-Guérin (BCG) and mitomycin C (MMC) are the two most commonly used intravesical therapies for non-muscle-invasive bladder cancer (NMIBC), yet variability in treatment outcomes and tolerability continues to challenge clinical decision-making. Updated comparisons reflecting current treatment protocols and adherence patterns are needed to inform practice. Objective The objective of this study is to evaluate and compare the efficacy and safety of intravesical BCG versus MMC in the contemporary treatment of NMIBC, focusing on recurrence, progression, and adverse effects over a 24-month follow-up. Methods This comparative study was conducted at the Khyber Teaching Hospital over a two-year period from January 2023 to December 2024. A total of 286 patients were enrolled, with 143 patients in each treatment group. Patients who had a complete transurethral resection of bladder tumor, were confirmed to have NMIBC, were at least 18 years old, and were eligible for intravesical therapy with either BCG or MMC were included in the study. Patients with muscle-invasive bladder cancer, BCG or MMC contraindications, active UTIs, severe immunosuppression, or serious comorbid diseases that might affect therapy results were excluded. Results The BCG group had much lower rates of cancer returning after 12 months (19 out of 143 patients, 13.29%, vs. 32 out of 143 patients, 22.38%; p = 0.037) and 24 months (34 out of 143 patients, 23.78%, vs. 49 out of 143 patients, 34.27%; p = 0.043), a longer average time before cancer returned (14.20 ± 4.80 months vs. 10.90 ± 5.30 months; p = 0.026), and less disease progression after 24 months (15 out of 143 patients, 10.49%, vs. 29 out of 143 patients, 20.28%; p = 0.021). Adverse effects were more frequent in the BCG group (n = 67, 46.85% vs. n = 58, 40.55%; p = 0.312), with fever (n = 19, 13.28% vs. n = 6, 4.19%; p = 0.012) and flu-like symptoms (n = 24, 16.78% vs. n = 8, 5.59%; p = 0.004) occurring more commonly. Conclusions BCG demonstrated superior efficacy over MMC in reducing recurrence and progression rates in patients with NMIBC, with a higher frequency of systemic adverse effects.