Type 2 diabetes mellitus (T2DM) and tuberculosis (TB) together impose a high disease burden in terms of both mortality and health economics worldwide. The objective of this study was to estimate the prevalence and risk factors of latent TB infection (LTBI) in patients with T2DM in Malaysia. A cross-sectional study was performed, and adult T2DM patients (n = 299) were included. Simple and multiple logistic regression analyses were performed to identify the LTBI-associated risk factors in patients with T2DM. Multiple logistic regression was used to estimate adjusted odds ratios (aOR) and 95% confidence intervals (CIs) between T2DM and LTBI and was adjusted for potential confounders. The prevalence of LTBI in patients with T2DM was 11.4% (95% CI: 8.0–15.0%). There was no significant difference in the socio-demographic characteristics between LTBI and non-LTBI subjects. No significant difference in the smoking status, the duration of smoking, and the duration of T2DM, HbA1c, or treatments was observed. Interestingly, a higher level of education was observed to be associated with a lower prevalence of LTBI in T2DM patients (aOR: 0.08, 95% CI: 0.01–0.70, p = 0.02). Although the prevalence of LTBI in T2DM was low, it is important to screen for it in T2DM patients due to the risk of developing severe active TB.