Background Young psychoactive substance users exhibit high-risk behaviours which can increase their risk to Hepatitis B infection. However, there is limited information on screening, and completion of the Hepatitis B vaccination schedule among young psychoactive substance users in informal settlements. Therefore, this study determined the factors associated with Hepatitis B screening, and completion of the Hepatitis B vaccination schedule among young psychoactive substance users in Kampala’s informal settlements, Uganda. Methods A cross-sectional study design was used. Respondent driven sampling was used to enroll 768 respondents from 12 informal settlements. Data were collected using a structured questionnaire and analysed using Stata version 14. A “modified” Poisson regression analysis was done to determine the factors associated with Hepatitis B screening while logistic regression was used to determine the factors associated with completion of the Hepatitis B vaccination schedule. Results Out of the 768 respondents, only 13.3% had ever screened for Hepatitis B and 2.7% had completed the Hepatitis B vaccine schedule. Being a female (aPR 1.61, 95% CI: 1.11-2.33), earning a monthly income >USD 136 (aPR 1.78, 95% CI: 1.11-2.86); completion of the Hepatitis B vaccination schedule (aPR 1.85, 95% CI: 1.26-2.70); lack of awareness about the recommended Hepatitis B vaccine dose (aPR 0.43, 95% CI: 0.27-0.68); and the belief that the Hepatitis B vaccine is effective in preventing Hepatitis B infection (aPR 3.67, 95% CI: 2.34-5.73) were associated with “ever screening” for Hepatitis B. Knowledge about the recommended Hepatitis B vaccine dose (aOR 0.06, 95% CI: 0.01-0.35); “ever screening” for hepatitis B (aOR 9.68, 95% CI: 2.17-43.16) and the belief that the hepatitis B vaccine is effective in preventing Hepatitis B infection (aOR 11.8, 95% CI: 1.13-110.14) were associated with completion of the Hepatitis B vaccination schedule. Conclusion Our findings indicate a low prevalence of Hepatitis B screening and completion of the Hepatitis B vaccination schedule among young psychoactive substance users in informal urban settings. It is evident that lack of awareness about Hepatitis B is associated with the low screening and vaccination rates. We recommend mass sensitisation of young psychoactive substance users in urban informal settlements on Hepatitis B.