Abstract Background Well-timed initiation of HIV therapy enhances life expectancy, decreases mortality and morbidity, and inhibits the transmission of HIV and complications related to it. The purpose of the present survey is to investigate the frequency and reasons for delayed initiation of anti-retroviral therapy (ART) and to determine its relationship with various socio-demographic variables and HIV-related characteristics. Methods The analysis is based on a cross-sectional study involving 355 people living with HIV (diagnosed by PCR) who were more than 18 years of age and not receiving HIV therapy before enrolment at the HIV clinics of two selected tertiary-care teaching hospitals in Lahore, Pakistan. In this study, delayed initiation of ART was defined as not attending the HIV management centre or a clinic for ART within 3 months of a confirmed diagnosis. The participants were selected using a systematic probability sampling technique. Bivariate logistic regression was performed using a backward stepwise technique to establish the variables related to delayed onset of HIV therapy. Factors significant at p ≤ 0.20 were considered for multivariate analysis, which was used to describe the association between independent factors and delayed initiation of treatment. Results Delayed onset of ART was observed in 28.5% of individuals. Factors such as no schooling (AOR = 5.92; 95% CI: 1.38–25.41; p = 0.017) and occasional household income (AOR = 3.88; 95% CI: 1.01–14.89; p = 0.048) were significantly associated with late onset of ART. Our research findings also indicated that the main reasons for late beginning of HIV therapy were: feeling healthy (45.5%), did not have time to go to the HIV treatment centre (42.6%), did not want to discuss HIV test result (37.6%), and fear of stigma and discrimination within their community (35.6%). Conclusions Late commencement of HIV therapy in Pakistan is common, and an improved connection is needed between identification of HIV and beginning of therapy. HIV management centres should counsel and monitor patients from the time of a positive HIV test result until they initiate therapy.