The Vaippar basin in southern India is economically important for rainfed and irrigated agriculture, mainly depending on the northeast monsoon (NEM) during October–December, and any changes in rainfall patterns directly affect crop ecosystems. This study aimed to analyze spatio-temporal rainfall changes using the monthly data from 13 scattered rain gauge stations in the Vaippar basin, India. They were converted into gridded rainfall data by creating 26 equally spaced grids with a spacing of 0.125° × 0.125° for the period between 1971 and 2019 through interpolation technique. Three methods, namely Simple Linear Regression (SLR), Mann–Kendell/modified Mann–Kendell (MK/MMK), and Sen’s Innovation trend analysis (ITA), were employed to detect trends and magnitudes for annual and seasonal gridded rainfall series. The results showed significant trends at 2.3%, 7.7%, and 44.6% of grid points using SLR, MK/MMK, and ITA methods, respectively. Notably, ITA analysis revealed significant trends in annual and NEM rainfall at 57.69% and 76.92% of the grid points, respectively, at a 5% significance level. The southwestern and central parts of the basin exhibited a higher number of significant upward trends in annual rainfall. Similarly for the NEM season, the south-eastern, central, and extreme southern parts experienced significant upward trend. The western part of the basin exhibited significantly upward trend with a slope value of 2.03 mm/year, while the central part showed non-significant downward trend with a slope value of −1.89 mm/year for the NEM series. This study used the advantage of ITA method, allowing for exploration of monotonic/non-monotonic trends, as well as subtrends of low, medium, and high rainfall segments within the series. The key findings of this study serve as a scientific report from a policy perspective, aiding in the preparation and management of extreme climate effects on land and water resources in the Vaipaar basin.