Understanding crop responses to climate is essential to cope with anticipated changes in temperature and precipitation. We investigated the climate–crop yield relationship and the impact of historical climate on yields of rice, maize and wheat in the Koshi basin of Nepal. The results show significant impact of growing season temperature and precipitation on crop production in the region. Rice, maize and wheat cultivated at altitudes below 1,100, 1,350 and 1,700 m amsl (above mean sea level), respectively, suffer from stress due to higher temperatures particularly during flowering and yield formation stages. Responses of crop yields to a unitary increment in growing season mean temperature vary from -6 to 16 %, -4 to 11 % and -12 to 3 % for rice, maize and wheat, respectively, depending on the location and elevation in the basin. In most parts of the basin, we observe warming trends in growing season mean temperatures of rice, maize and wheat over the last few decades with clear evidence of negative impacts on yields. However, at some high-elevation areas, positive impacts of warming are also observed on rice and maize yields. If the observed trends in temperature continue in future, the impact is likely to be mostly negative on crop production in the basin. However, crop production may gain from the warming at relatively higher altitudes provided other conditions, e.g., water availability, soil fertility, are favorable.