Concrete strength is dependent upon not only the water to cement ratio but also different constituents of the concrete. The inclusion of natural zeolite (NZ) as an effective supplementary cementitious material (SCM) creates reproductions through pozzolanic reaction, which improves the mechanical properties and durability of concrete. The paper is aimed at studying the feasibility of applying Gene Expression Programming (GEP) method for predicting the compressive strength and electrical resistivity of concrete. Hence, in this research, 54 mix designs containing three water to binder (W/B) ratios, three binder contents, as well as six different replacement levels of NZ were first constructed. Thereafter, the compressive strength and electrical resistivity of the manufactured specimens at various ages were measured. In order to predict the two properties, various models were proposed by using GEP. Eight parameters including the specimen age and the cement, water, gravel (separated to G20 and G10), sand, NZ, and superplasticizer contents were considered as input variables. The experimental results showed that 7.5–10% of NZ had an incremental effect on compressive strength development in the long-term and the inclusion of 20% NZ led to a considerable increase in the electrical resistivity of the mixes, particularly at higher ages. Furthermore, comparing the measured properties with their predicted counterparts indicated the great potential of the proposed GEP models for predicting both compressive strength and electrical resistivity of concrete containing NZ.