Annual and seasonal rainfall trends in the Limbang River Basin (LRB), located in the equatorial tropics of Malaysian Borneo, have been characterised through Mann-Kendall and Spearman’s Rho non-parametric tests. Rainfall from 13 rain gauge stations in the LRB for the period 1948–2016 was examined in the present study. Basic statistical analysis of rainfall in the region indicates normal distribution, low missing percentage and homogenous characteristics of precipitation. Annual and seasonal rainfall in the LRB shows spatial variation while considering different rain gauge stations. In annual rainfall, eight stations showed a decreasing trend and five stations showed an increasing trend. Rain gauge stations which showed a statistically significant increase in annual rainfall were Limbang DID (2.77 and 2.85 mm/year) and Long Napir (3.65 and 3.77 mm/year). In recognising the two annual monsoon seasons in this area, a significant increase in rainfall was noticed in Long Napir (2.79 and 2.88 mm/year) during the Southwest monsoon (SWM) period. During the Northeast monsoon (NEM), along with Long Napir (3.90 and 3.95 mm/year), Limbang DID (2.86 and 3.02 mm/year), Pandaruan (1.82 and 1.87 mm/year) and Medamit Nanga (1.93 and 2.00 mm/year) also showed a significant increase in rainfall. At the same time, a distinct trend was noticed in rainfall amounts during the inter-monsoon (IM) periods. During the first inter-monsoon month (April), seven rain gauge stations showed an increasing trend in rainfall, whereas in the second inter-monsoon month (October), nine stations showed a decreasing rainfall trend. In April, Long Napir (1.86 and 1.95 mm/year) indicated a significant increasing trend, whereas in the month of October, the rain gauge station at Ukong showed a significant decreasing trend (− 2.45 and − 2.37 mm/year). Though minor spatial changes in trend characteristics were observed among the rain gauge stations, the LRB as a whole showed a consistent increasing (significant and non-significant) trend in annual and seasonal rainfall.