Introduction The hijra and transgender (H/TG) population in India is vulnerable to HIV/AIDS. India had instituted a targeted intervention (TI) program to reduce this vulnerability. We aimed to measure the effectiveness of the TI program for H/TG. Materials and Methods The National Integrated Behavioral and Biological Survey (IBBS) was carried out in 2014-15. H/TG data from IBBS was analyzed. Bivariate and multivariate logistic regression were used to calculate the unadjusted and adjusted odds ratios with 95% confidence interval. Condom use during the last sexual intercourse, and the consistent condom use in the last one month were considered as indicators of program effectiveness. The Propensity Score Matching (PSM) method was used to assess the effectiveness. Results We found that the participants who had received condoms from peer educator/outreach worker were 1.74 and 1.40 times more likely to use condoms in the last sexual intercourse (aOR: 1.74, CI: 1.35 – 2.26) and consistent condom use in the last one month (aOR: 1.40, CI: 1.12 – 1.74) respectively compared to the participants who did not receive the condom. The matched-samples estimate (i.e., average treatment effect on treated) for the condom use during the last sexual intercourse increased by 13.0%, i.e., 0.13 (CI; 0.08 - 0.18) and consistent condom use in the last one month increased by 5.0%, i.e., 0.05 (CI; 0.00 – 0.10) among those who had received condoms from the peer educator/outreach worker compared with those who had not received condom, respectively. Conclusions The TI program intervention for H/TG was effective in reducing HIV risk behavior as evidenced by increase in use of condom during last sexual intercourse, and consistent condom use in the last one month.