The prevalence and treatment of chlamydia (CT) and gonorrhea (GC) at school-based clinics (SBCs) requires revisiting. To assess whether clinic type influences CT/GC testing and treatment for minors (individuals 13–17 years of age), our study compared four SBCs with five family planning clinics (FPCs) in the Houston, Harris County metropolitan area of Texas, USA for: (1) the prevalence of CT/GC infection (pre-COVID-19 and during COVID-19); (2) treatment rates at the last positive diagnosis; and (3) the time, in days, from testing-to-diagnosis and testing-to-treatment. Between January 2019 and December 2020, 2439 unique patients (1579 at SBCs, 860 at FPCs) were seen. Of the 1924 tests obtained, 39.2% and 15.9% were positive for CT and GC, respectively. The prevalence of CT and GC at SBCs was similar prior to COVID-19 vs. during the COVID-19 pandemic. SBCs were able to provide treatment significantly faster after diagnosis (mean, 6.07 days; 95% CI, 3.22–8.90; 94.7% were within 30 days) than FPCs (mean, 17.60 days; 95% CI, 10.15–25.12; 84.7% were within 30 days) (p = 0.0257). This comparison within our large clinic system, with consistent clinical management protocols, suggests that SBC care may be critical to ensuring optimal sexually transmitted infection management in minors.