The low prevalence of condom usage among youth with Human Immunodeficiency Virus/Sexually Transmitted Diseases (HIV/STDs) is a concern. Condom use self-efficacy has been identified as a significant predictor of condom usage. This cross-sectional study examines the prevalence of good condom usage and its association with condom use self-efficacy among Malaysian urban youth, aged between 18 to 24 years old attending HIV/STDs clinics in primary-care settings, Selangor. Utilising the Harmonised Malay version of Condom Use Self-Efficacy Scale (CUSES M-H) questionnaire, the data from 218 responders were analysed using univariate and multiple logistic regression. The prevalence of good condom usage was 61% (95% CI: 54%, 68%). The average mean score of condom use self-efficacy was 3.07. Condom use self-efficacy was divided into four subscales of mechanics, perceived barriers, assertiveness and intoxicants. The assertiveness subscale had the highest average mean score of 3.42, while the intoxicant subscale score had the lowest average mean score of 2.24. Good condom usage was significantly associated with condom use during first sexual intercourse (aOR = 5.81, 95% CI: 1.97, 17.14), duration diagnosis of HIV/STDs of more than 12 months (aOR = 6.40, 95% CI: 2.30, 17.86) and the high assertiveness subscale score (aOR = 1.19, 95% CI: 1.03, 1.36). A behavioural change campaign that targets high-risk youth in primary care settings could promote condom use self-efficacy particularly assertiveness to increase condom usage among the youth.