The present study is to explore the feasibility of GRACE‐based estimation of a groundwater storage change in a data‐poor region using a case study of the Ngadda catchment in the Lake Chad Basin. Although the Ngadda catchment has only one set of in situ time series data of groundwater from 2006 to 2009 and a limited number of groundwater measurements in 2005 and 2009, GRACE‐based groundwater storage change can be evaluated against the in situ groundwater measurements combined with specific yield data. The cross‐correlation analysis in the Ngadda catchment shows that maximum rainfall reached in July and August, whereas both the maximum total water storage anomaly and the maximum groundwater storage anomaly occurred 2months later. Whereas the mean annual amplitude of total water storage anomaly is about 17cm from both the average total water storage anomaly from three mascon products and the one from three spherical harmonic products, the mean annual amplitude of soil moisture storage anomaly is substantially varied from 5.58cm for CLM to about 14cm for NOAH and Mosaic. The goodness‐of‐fit tests show that CLM soil moisture produces the closest estimation of groundwater storage anomaly to the in situ groundwater measurements. The present study shows that GRACE‐based estimation for groundwater storage anomaly can be a cost‐effective and alternative tool to observe how groundwater changes in a basin scale under the limitation of modelling and in situ data availability.