Abstract Background Taiwan has integrated the previous vertical tuberculosis (TB) control system into the general health care system. With the phase out of the specialized TB care system and the declining TB incidence, it is likely that clinical workers become less familiar with the presentation of TB, resulting in delay in TB diagnosis and treatment. Methods We used the detailed information of health care visits in the Taiwan National Health Insurance database to analyze the temporal pattern of the health system delay (HSD) among 3,117 patients with TB between 2003 and 2010. Results The median HSD was 29 days (interquartile range 5–73 days), and the median delay increased from 26 days in 2003 to 33.5 days in 2008, thereafter slightly decreased to 32 days in 2010. Patient factors associated with a longer HSD included: aged 45–64 and ≧65 years (as compared to aged <30 years); females (as compared to males); an initial visit as an outpatient (as compared to an inpatient). Provider factors were an initial visit to a provider not specialized in TB (as compared to a TB-related provider), to a primary care clinic or to a medical center (as compared to a district hospital), and in Central region, Northern region, KaoPing region, Southern region and Taipei region (as compared to in Eastern region). Longer distances from the point of initial visit to that of treatment were associated with longer HSD. Patients who switched among different levels or different types of medical care services during their illness exhibited the longest HSD. Conclusions In countries where the TB care systems are being restructured from a vertical to a horizontal system, it is critical to monitor HSD and be aware of its increase. The potential increase in the HSD from 2003 to 2008 observed in this study is concerning and the decline of HSD after 2008 might be attributed to the launch of contact investigation. Our results call for actions to improve the efficiency of TB diagnosis in the health care system and to increase the awareness of TB among physicians and the general public.