Background: Sexually transmitted infections (STIs) are increasing among adolescents and young adults (AYA) across the United States. However, data are scarce on trends in condom use, number of partners, and other STI risk factors among AYA. The present study evaluated associations between sexual behaviors and STI diagnoses over time among AYA. Methods: We evaluated linked encounters of AYA aged 13–26 attending an urban Northeast public STI clinic from 2013–2017. Demographics, risk behaviors, self-reported past year and lifetime STI, and STI diagnosis during clinic encounter (positive test for urine, oral, or anal chlamydia; urine, oral, or anal gonorrhea; urine trichomonas; HIV; and syphilis) were extracted from electronic health records. We estimated prevalence and performed trend analyses of the repeated cross-sectional data. Cochran–Armitage and Kruskal–Wallis trend test were conducted for categorical and continuous variables, respectively. Results: Among 3822 encounters, clinical STIs demonstrated statistically significant increases including chlamydia (+9%, p = 0.001), gonorrhea (+5%, p = 0.008), and syphilis (+3%, p = 0.006) all of which significantly increased over time, as did any STI (+10%, p < 0.001). HIV and trichomonas rates remained low and unchanged. Self-reported STI increased as well, both past year (+9%) and lifetime (+14%). Greater proportions of AYA reported multiple partners (+9%, p < 0.001), and condomless oral (+12%, p = 0.001) and vaginal/anal (+7%, p = 0.001) sex. Conclusion: Among AYA presenting to a STI clinic, the proportion who engaged in condomless sex and had multiple partners increased over a 5 year period, which corresponded to increased STI prevalence during this period. Preventions efforts for AYA should continue to emphasize the importance of condoms and partner selection.