In El Oued, southern Algeria, the traditional Mini-Centre Pivot System (MCPS) is widely used for the irrigation of agricultural crops, and its use has been growing continuously. However, these systems have a constant nozzle diameter along the lateral pipe, which affects productivity directly, besides decreasing both the quantity and quality of agricultural products by irrigation heterogeneity. Therefore, optimising the design of the MCPS nozzles is linked strongly to the desired uniform irrigation. This study aims to determine the optimal configuration of nozzles for high irrigation uniformity. To achieve this goal, a genetic algorithm was used for maximising the uniformity of MCPS-mediated irrigation. The optimisation is carried out according to water distribution modelling, calculation of the Heermann and Hein uniformity coefficient (CUH), and existing nozzle diameters. To verify the accuracy of the proposed model, three existing MCPS (60 m, 50 m, and 46 m in length) are investigated experimentally. The developed code findings in terms of CUH are in agreement with those obtained by experimental tests. The analysis indicated that the nozzle diameter should vary from 5 to 15 mm along the lateral pipe. In these optimal conditions, the CUH was improved by 29.77%, 33.99%, and 19.36%, respectively, for the existing 60, 50, and 46 m irrigation systems. The most obvious findings to emerge from this study is that using a genetic algorithm to optimise the design based on the nozzle size improves water application uniformity by more than 19% in terms of the CUH.