Background: Chemsex is the use of illicit drugs—particularly methamphetamine, gamma hydroxybutyrate (GHB), and gamma-butyrolactone (GBL)—to enhance sexual activity. Chemsex, which occurs primarily among communities of men who have sex with men (MSM), is associated with greater HIV risk behaviors, including multiple sex partners, group sex, condomless sex, and injection drug use. Despite evidence showing chemsex engagement among Malaysian MSM, there is a paucity of research on chemsex among MSM in Malaysia. Methods: This cross-sectional study was conducted through an online survey (August to September 2021) among 870 Malaysian MSM. Participants were recruited through targeted advertisements on social networks. We collected information regarding participants’ recent (<6 months) engagement in chemsex, demographic characteristics, psychosocial factors, pre-exposure prophylaxis (PrEP) knowledge and history, and recent sexual- and drug-related behavior. Multivariable logistic regression was used to identify factors associated with recent (<6 months) chemsex engagement. Results: Just under 1 in 10 (9.0%) of participants reported having engaged in chemsex in the previous six months. More than two-thirds of participants (69.1%) had not disclosed their sexual orientation to anyone in their family and 35.2% reported moderate to severe depressive symptoms. Multivariable analysis found that recent injection drug use (adjusted odds ratio: aOR = 6.61; 95% confidence interval: CI, 2.30–19.03), having shared pre-exposure prophylaxis (PrEP) with someone else (aOR = 5.60; 95% CI, 1.76–17.77), higher perceived HIV risk (aOR = 3.15; 95% CI, 1.25–7.93), knowing someone using PrEP (aOR = 2.93; 95% CI, 1.62–5.31), recent engagement in transactional sex (aOR = 2.38; 95% CI, 1.06–5.39), having a recent STI diagnosis (aOR = 2.36; 95% CI, 1.25–4.44), recent engagement in anal sex (aOR = 2.21; 95% CI, 1.07–4.57), and recent sexual intercourse with an HIV-positive partner (aOR = 2.09; 95% CI, 1.07–4.08) were associated with recent engagement in chemsex. Conclusions: Malaysian MSM who practice chemsex are vulnerable to several HIV risk factors, such as transactional sex, HIV-positive sexual partners, and injection drug use. There is an urgent need for programs that integrate drug, sexual health, and mental health services, with a focus on harm reduction (e.g., condoms, access to and utilization of HIV testing and PrEP services, drug knowledge, and safer drug use) tailored for MSM who practice chemsex.