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Abstract Introduction There is a high teenage pregnancy in Lake Victoria Island and Mountain districts of Uganda. Teenage pregnancy is highly associated with abortions, infant and maternal mortality, high rate of unemployment, school failure and drop-outs and limited future career opportunities. This paper identifies and explains the factors influencing teenage pregnancy in Uganda Lake Victoria Island shoreline area and mountain districts. Methods The analysis focused on 405 girls aged 15–19 years, generated from the 2016 Uganda demographic and Health Survey. Odds ratios with 95% confidence interval and p-values were computed using appropriate logistic regression models to determine the presence and strength of associations between the teenage pregnancy and independent variables. Results Age, residence, secondary or higher education level, female-headed households, marital status (married), occupation, wealth index(rich quintile), and knowledge of ovulation cycle were found to have statistically significant associations with teenage pregnancy. Conclusion Increased age, rural residence, occupation(not working), and knowledge of ovulation cycle were statistically significant predisposing factors of teenage pregnancy in Uganda Lake Victoria Island shoreline area and mountain districts. Teenagers in these study areas should be provided with sexual education as well as teenage-friendly health services at health facilities that include a wide range of options, as well as medically accurate counselling and information could mitigate teenage pregnancy.