At present, much of the attention within tuberculosis (TB) management is spent on microbiological cure, and its impact on health-related quality of life (HRQoL) is either undervalued or seldom considered. The aim of this study was to evaluate the impact of TB treatment on HRQoL of new smear positive pulmonary tuberculosis (PTB) patients. Moreover, we also aimed to determine whether the selected socio-demographic and clinical variables were predictive of variability in the HRQoL scores over time. This was a prospective follow-up of new smear positive PTB patients who were diagnosed at the chest clinic of Penang General Hospital between March 2010 and February 2011. All eligible patients (i.e., a new case of smear positive PTB, literate and aged 18 years or above) were asked to self-complete the SF-36v2 questionnaire at the start of their treatment, and then subsequently after the intensive phase and at the end of the treatment. A score on a health domain or component summary measure that was less than 47 norm-based scoring (NBS) point was considered indicative of impaired function within that health domain or dimension. Likewise, an individual having mental component summary (MCS) score ≤ 42 NBS point was considered to be at the risk of depression. Repeated measures ANOVA test was performed to examine how the summary scores varied over time, and to determine whether independent variables were predictive of variability in the physical component summary (PCS) and MCS scores over time. A total of 216 patients completed the SF-36v2 questionnaire at the start of their treatment. Out of these, 177 and 153 completed the questionnaire at the second and third follow-ups, respectively. The mean PCS scores at the start of the treatment, after the intensive phase and at the end of treatment were 41.9 (SD 5.1), 45.8 (SD 4.8) and 46.0 (SD 6.9), respectively. Similarly, the mean MCS scores at the start of the treatment, after the intensive phase and at the end of the treatment were 39.9 (SD 7.3), 45.0 (SD 6.8) and 46.8 (SD 7.8), respectively. More than 23% of the patients were at the risk of depression at the end of their TB treatment. Patient's age and being a smoker were predictive of differences in the PCS scores. Similarly, monthly income, being a smoker and TB-related symptoms at the start of the treatment were predictive of differences in the MCS scores. Although HRQoL improved with the treatment, the scores on component summary measures showed compromised physical and mental health among study patients even at the end of their TB treatment.