Background The COVID-19 pandemic related restrictions and lockdown measures had compromised the routine delivery and access of sexual and reproductive health and rights services to the population including the teenage girls. However, the teenage pregnancy rates during COVID-19 pandemic period were poorly documented. This study aimed at determining the prevalence and the factors associated with teenage pregnancy among in-school teenage girls during the COVID-19 pandemic period in Hoima District Uganda. Methods This was a descriptive cross-sectional study that employed quantitative research methods. A total of 314 in-school teenage girls aged 13–19 years were selected using a multi-stage sampling techniques. Interviewer-administered questionnaires were used to collect the data from the participant’s homes during the period December 2021-January 2022. Data analysis was done using univariate, bi-variate, and multivariate. Results The prevalence of teenage pregnancy among the in-school teenage girls in Hoima district Uganda was 30.6% [96/314]. Higher teenage pregnancy rates were prevalent among the unmarried teenage girls [aOR: 9.6; 95%CI: 4.64–19.87; p = 0.000], teenage girls studying from boarding schools [aOR 2.83, 95%CI 1.36–5.86, p = 0.005], contraceptive non-users [aOR: 2.54; 95%CI: 1.12–5.4; p = 0.015] and teenage girls involved in sex trade [aOR 3.16, 95%CI 1.5–6.7, p = 0.003]. The factors associated with the reduced likelihood for teenage pregnancy included being an adult teenage girl aged 18–19 years [aOR: 0.15; 95%CI: 0.07–0.32; p = 0.000] and not receiving sex education during the period [aOR 0.36, 95%CI 0.13–0.62, p = 0.024]. Conclusion The results indicated that 3 out of 10 in-school teenage girls from Hoima district Uganda got pregnant during the COVID-19 pandemic period of 2021. Teenage pregnancy was prevalent among teenage girls who don’t use modern contraceptive methods and those involved in sex trade. Teenage pregnancy was however, less prevalent among adult teenage girls aged 18–19 years. The findings point to the need for health stakeholders to innovate creative policies, contingency plans and programmes aimed at delaying age for sexual activities, increasing contraceptive use and minimizing pregnancy risk from sex trade among in-school teenage girls during COVID-19 pandemics.