While ample evidence exists regarding the use of active amphetamine-type stimulants (ATS) among sex workers, the impact of ATS use has yet to be characterized among the transgender population in Malaysia. Our aim is to highlight and assess health-related factors associated with ATS use among transgender women in Malaysia. A total of 361 transgender women completed a cross-sectional survey regarding their attitude towards PrEP knowledge and use for HIV prevention. The original study explored a myriad of health-related topics including active ATS use. Data was analyzed using logistic regression analyses to determine factors associated with active ATS use. Most of the participants were between 25-40 years old (57.3%), ethnically identified as Malay (75%), and single (67.6%). We found that 10.2% of the participants were actively using ATS. On a multivariate level, hormone therapy use was associated with reduced odds of active ATS use (aOR = 0.364; 95% CI = 0.169, 0.784) and was positively associated with a history of drug related arrest (aOR = 4.604; 95%CI = 1.813, 11.691). Our findings show a high prevalence of active ATS use among transgender women in Malaysia, in addition to its correlation to other health- related factors. Interestingly, we found that trans women who were actively using hormone therapy, were less likely to engage in active ATS use. This relationship should be explored further along with the relationship between incarceration history. In addition, further prevention strategies and efforts are needed to decrease ATS use among transgender women in Malaysia.