Abstract Background The prevalence of chronic kidney disease (CKD) in Malaysia was 9.07% in 2011. We aim to determine the current CKD prevalence in Malaysia and its associated risk factors. Methods A population-based study was conducted on a total of 890 respondents who were representative of the adult population in Malaysia, i.e., aged ≥18 years old. Respondents were randomly selected using a stratified cluster method. The estimated glomerular filtration rate (eGFR) was estimated from calibrated serum creatinine using the CKD-EPI equation. CKD was defined as eGFR < 60 ml/min/1.73m2 or the presence of persistent albuminuria if eGFR ≥60 ml/min/1.73m2. Results Our study shows that the prevalence of CKD in Malaysia was 15.48% (95% CI: 12.30, 19.31) in 2018, an increase compared to the year 2011 when the prevalence of CKD was 9.07%. An estimated 3.85% had stage 1 CKD, 4.82% had stage 2 CKD, and 6.48% had stage 3 CKD, while 0.33% had stage 4–5 CKD. Hypertension (aOR 3.72), diabetes mellitus (aOR 3.32), increasing BMI (aOR 1.06), and increasing age (aOR 1.06) were significantly associated with CKD. Conclusion Our study has shown that CKD has become one of the leading public health issues in Malaysia. Thus, there is an urgent need to screen for CKD and prevent its progression, associated morbidity, and mortality at the national level.