Nowadays, with increasing energy consumption in distribution networks and the demand of consumers to buy highly reliable power, it is of high importance to establish adaptation between protection and operation of the power system. Therefore, this paper analyses the effect of optimal reconfiguration of the smart distribution system in the presence of wind and solar renewable resources under fault conditions. Uncertainties of load and production of renewable resources are studied as well. In the proposed model, the optimal topology of the distribution network is obtained to minimise the system losses. Also, features of the distribution network protection systems, including constraints on the coordination and performance of the equipment, are added to the reconfiguration problem. According to linearisation, the proposed model becomes a mixed-integer linear programming. Several case studies are carried out on a modified 33-bus network using GAMS and MATLAB to show the effectiveness and robustness of the proposed model on both operational and protection coordination. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.