The exact influence of the COVID-19 pandemic on sexual intercourse and usage of contraception remains largely uncharted territory. To bridge this gap in knowledge, we conducted a comprehensive, cross-sectional examination of long-term trends in the prevalence of sexual intercourse and usage of contraception among South Korean adolescents from 2006 to 2022. In our research, we drew upon data encompassing 1,138,799 South Korean adolescents aged 12 to 18years, derived from the Korean Youth Risk Behavior Web-based Survey (KYRBS) over a period spanning from 2006 to 2022. We focused on the prevalence of sexual intercourse, contraception utilization, and the underlying associated factors among this demographic. The KYRBS data was collected using a complex sampling strategy to determine the national prevalence estimates and shifts in prevalence before (2006-2019) and during (2020-2022) the COVID-19 pandemic era. During the pre-pandemic period, a decrease in adolescent sexual intercourse was observed (6.34% in 2006, 5.53% in 2012, and 5.87% in 2019). However, in the post-pandemic period (2020-2022), there was a surge in sexual intercourse (4.55% in 2020 and 6.20% in 2022). This evident alteration in sexual intercourse trajectory between pre- and post-pandemic periods was statistically significant [βdiff, 0.950; 95% confidence interval (CI), 0.756-1.144]. Regarding contraceptive use among South Korean adolescents, there was an increase in the pre-COVID-19 pandemic phase across all demographic segments (14.61% in 2006, 22.30% in 2012, and 47.69% in 2022) but a notable decline when compared with the pre- and post-pandemic periods (βdiff, -0.319; 95% CI, -0.454 to -0.184). Additionally, during the study period, a decrease in sexual intercourse was observed in the pre-pandemic period (β, -0.129; 95% CI, -0.148 to -0.110), followed by an increase in the post-pandemic period (β, 0.821; 95% CI, 0.627 to 1.014). This shift is highlighted by an effect size of 0.96 [weighted odds ratio (wOR); 95% CI, 0.92 to 1.00], indicating a substantial change in adolescent sexual behaviors across study periods. The increase in sexual intercourse and decrease in usage of contraception observed in our study between the pre- and post-COVID-19 periods suggests a potential threat to sexual health among South Korean adolescents. This trend emphasizes the ongoing necessity of raising awareness about adolescent sexual behavior in South Korea.