Objectives To determine the prevalence and risk factors of Blastocystis among underprivileged communities living in rural Malaysia. Methods This cross-sectional study was conducted among 253 participants aged between 1 and 85 years. Stool samples were examined using Wheatley's trichrome stain after in-vitro cultivation in Jones' medium to detect the presence of Blastocystis. Information pertaining to the demography, socioeconomic and environment were collected using pre-validated questionnaires. Results The total prevalence of Blastocystis infection was 40.7%. The multiple logistic regression analysis revealed that age ≥15 years (OR = 2.72; 95% CI = 1.47–5.04) and presence of infected family members (OR = 8.56; 95% CI = 4.47–16.38) were the significant risk factors associated with blastocystosis in these communities. Conclusions Blastocystosis is revealed through this study to be still prevalent among Orang Asli communities in rural Malaysia. The two main approaches that should be implemented by the public health authority in battling this infection would be the screening of other family members and giving treatment to the infected individuals. Moreover, it is imperative for health education on good personal and food hygiene practices are provided in order to reduce the morbidity and transmission of Blastocystis infection among the Orang Asli in their communities meaningfully.