The increase of anthropogenic activities has triggered global sea level rise to threaten many low-lying and unprotected coastal areas. Without measures, global sea levels will continue to rise at an accelerating rate in the 21st century. This paper quantifies sea level trends around the Malaysian seas using measurements from multiple altimeter missions over 1993–2015. Sea level anomalies (SLAs) are determined using data from the Radar Altimeter Database System (RADS) covering 8 altimeter missions. We use an enhanced processing strategy to optimize sea surface heights from RADS for the derivation of SLAs, including filtering, data gridding and moving average. Tidal height measurements at eight tide gauge stations around Peninsular Malaysia and East Malaysia are used to assess SLAs from altimetry. Our assessment results in similar patterns of SLAs, high correlation coefficients (>0.9) and small (few cm) root mean square differences (RMSE) between SLAs from altimetry and tide gauges over the same period. Sea level trends are determined by the robust fit regression analysis for the SLA time series. Our result shows that sea level rise trends around Malaysia range from 3.27 ± 0.12 mm yr−1 off eastern Malaysia to 4.95 ± 0.15 mm yr−1 west of Malaysia. Over 1993–2015, the mean rising rate around Malaysia is 4.22 ± 0.12 mm yr−1, and the cumulative sea level rise is 0.05 m. This paper predicts the impact of such rising sea levels on environment, urban planning and climatology in the coastal areas of Malaysia.