Salinity is a major problem in agriculture because it can alter the metabolism of plants and affect crop yield. This study aimed to evaluate the effect of NaCl on growth, key antioxidants and changes in the expression of genes encoding antioxidant enzymes. Two popcorn genotypes, IAC125 and UFMV2, experienced reduction in growth as the salt concentration increased. Increase in chlorophyll content and damage to the plasma membrane was observed. Consequently, changes in osmotic activity led to reduced water content in the leaves. Increased concentration of salt increased the activity of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) in two popcorn genotypes but maximum activity was observed in the IAC125 genotype. Such enzymatic activities occur in order to maintain the levels of lipid peroxidation under salt stress, indicating that this genotype is tolerant to salinity conditions. The ZmAPX, ZmCAT, ZmSOD (Cu/Zn) and ZmSOD (Mn) genes increased their expression as salinity increased. The ZmSOD (Fe) gene was highly regulated in the IAC125 genotype under salt stress, but low regulation was observed in the UFM2 genotype, regardless of the salt concentration. The enhancement in tolerance against salt stress indicates that the genes involved in the antioxidative process are triggered by oxidative stress induced by abiotic stresses. These results showed that the popcorn varieties have different levels of salt tolerance due to the differential expression pattern of the antioxidant genes. The up-regulation of antioxidant enzymatic activity could lead to increased scavenging of excessive free radicals and reduce oxidative stress.