This study investigates the trend in monthly and annual rainfall, minimum and maximum temperature (T_min and T_max) using the Mann–Kendall (MK) test and Sen’s slope (SS) method and evaluates the significance of their variability for maize, sorghum and millet yields in northern Togo employing multiple regression analysis. The historical data of Kara, Niamtougou, Mango and Dapaong weather stations from 1977 to 2012 were used. Four non-parametric methods—Alexandersson’s Standard Normal Homogeneity Test (SNHT), Buishand’s Range Test (BRT), Pettitt’s Test (PT) and Von Neumann’s Ratio Test (VNRT)—were applied to detect homogeneity in the data. For the data which were serially correlated, a modified version of the MK test (pre-whitening) was utilised. Results showed an increasing trend in the annual rainfall in all four locations. However, this trend was only significant at Dapaong (p < 0.1). There was an increasing trend in T_max at Kara, Mango and Niamtougou, unlike Dapaong where T_max revealed a significant decreasing trend (p < 0.01). Similarly, there was an increasing trend in T_min at Kara, Mango and Dapaong, unlike Niamtougou where T_min showed a non-significant decreasing trend (p > 0.05). Rainfall in Dapaong was found to have increased (7.79 mm/year) more than the other locations such as Kara (2.20 mm/year), Niamtougou (4.57 mm/year) and Mango (0.67 mm). T_max increased by 0.13, 0.13 and 0.32 °C per decade at Kara, Niamtougou and Mango, respectively, and decreased by 0.20 per decade in Dapaong. Likewise, T_min increased by 0.07, 0.20 and 0.02 °C per decade at Kara, Mango and Dapaong, respectively, and decreased by 0.01 °C per decade at Niamtougou. Results of multiple regression analysis revealed nonlinear yield responses to changes in rainfall and temperature. Rainfall and temperature variability affects rainfed cereal crops production, but the effects vary across crops. The temperature has a positive effect on maize yield in Kara, Niamtougou and Mango but a negative effect on sorghum in Niamtougou and millet in Dapaong, while rainfall has a negative effect on maize yield in Niamtougou and Dapaong and millet yield in Mango. In all locations, rainfall and temperature variability has a significant effect on the cereal crop yields. There is, therefore, a need to adopt some adaptation strategies for sustainable agricultural production in northern Togo.