In this study, the effects of nano-CuO (NC) on engineering properties of fibre-reinforced mortars incorporating metakaolin (MK) were investigated. The effects of polypropylene fibre (PP) were also examined. A total of twenty-six mixtures were prepared. The experimental results were compared with numerical results obtained by adaptive neuro-fuzzy inference system (ANFIS) and Primal Estimated sub-GrAdient Solver for SVM (Pegasos) algorithm. Scanning Electron Microscope (SEM) was also employed to investigate the microstructure of the cement matrix. The mechanical test results showed that both compressive and flexural strengths of cement mortars decreased with the increase of MK content, however the strength values increased significantly with increasing NC content in the mixture. The water absorption of samples decreased remarkably with increasing NC particles in the mixture. When PP fibres were added, the strengths of cement mortars were further enhanced accompanied with lower water absorption values. The addition of 2 wt % and 3 wt % nanoparticles in cement mortar led to a positive contribution to strength and resistance to water absorption. Mixture of PP-MK10NC3 indicated the best results for both compressive and flexural strengths at 28 and 90 days. SEM images illustrated that the morphology of cement matrix became more porous with increasing MK content, but the porosity reduced with the inclusion of NC. In addition, it is evident from the SEM images that more cement hydration products adhered onto the surface of fibres, which would improve the fibre–matrix interface. The numerical results obtained by ANFIS and Pegasos were close to the experimental results. The value of R2 obtained for each data set (validate, test and train) was higher than 0.90 and the values of mean absolute percentage error (MAPE) and the relative root mean squared error (PRMSE) were near zero. The ANFIS and Pegasos models can be used to predict the mechanical properties and water absorptions of fibre-reinforced mortars with MK and NC.