A major strategy for preventing transmission of HIV and other STIs is the consistent use of condoms during sexual intercourse. Condom use among youths is particularly important to reduce the number of new cases and the national prevalence. Although a number of studies have established an association between condom use at one’s sexual debut and future condom use, few studies have explored this association over time, and whether the results are generalizable across multiple locations. This multi time point, multi district study assesses the relationship between sexual debut and condom use and consistent use of condoms thereafter. Uganda has used Lot Quality Assurance Sampling surveys since 2003 to monitor district level HIV programs and improve access to HIV health services. This study includes 4518 sexually active youths interviewed at five time points (2003–2010) in up to 23 districts located across Uganda. Using logistic regression, we measured the association of condom use at first sexual intercourse on recent condom usage, controlling for several factors including: age, sex, education, marital status, age at first intercourse, geographical location, and survey year. The odds of condom use at last intercourse, using a condom at last intercourse with a non-regular partner, and consistently using a condom are, respectively, 9.63 (95%WaldCI = 8.03–11.56), 3.48 (95%WaldCI = 2.27–5.33), and 11.12 (95%WaldCI = 8.95–13.81) times more likely for those individuals using condoms during their sexual debut. The results suggest that HIV prevention programs should encourage condom use among youth during sexual debut. Success with this outcome may have a lasting influence on preventing HIV and other STIs later in life.