Background Worldwide, about 11% of Tuberculosis (TB) cases occur in people living with HIV (PLHIV) and it is the leading cause of death in this population. An important step towards reducing the incidence and mortality of TB in PLHIV is to reduce the time from onset of symptoms to treatment. Factors related to TB treatment delay therefore need to be understood. Methods Using data from a prospective cohort study of patients diagnosed with TB at the National Institute of Infectious Disease, at the Oswaldo Cruz Foundation, Rio de Janeiro, Brazil we conducted a survival analysis to identify factors associated with patient and health care treatment delay. In our analysis we included patients who were co-infected with TB and HIV (n = 201). Patients were followed during the course of their TB treatment and information regarding duration of symptoms, sociodemographics and clinical characteristics were collected at the baseline visit. Results The median time from onset of initial symptoms to prescription of TB treatment (total delay) was 82 days. From initiation of symptoms to first visit at INI clinic (patient delay), the median was 51 days. From first visit to initiation of treatment (health care delay) the median was 16 days. Illiteracy was associated with greater patient delay [Hazard Ratio (HR) = 2.25, CI 95% 1.29–3.94]. Having had a previous episode of TB (HR = 0.53, CI 95% 0.37–0.74) and being married (HR = 0.71, CI 95% 0.54–0.94) were inversely related to patient delay. Illiteracy was also associated with greater health care delay (HR = 2.83, CI 95% 1.25–5.47) in contrast to high viral load (HR = 0.37, CI 95% 0.24–0.54) and weight loss greater than 10% (HR = 0.54, CI 95% 0.37–0.8), both of which were inversely related to health care delay. Conclusions This study highlights the existence of factors that lead to greater risk of delayed treatment of TB among patients co-infected with HIV and TB. These include factors that can be assessed through targeted interventions which have implications for improving treatment outcomes and, through reduced duration of infectiousness, reduce the incidence of TB in Brazil.