Pakchoi (Brassica campestris ssp. chinensis) is one of the most popular leafy vegetables, whose production is negatively affected by high NaCl concentration in the soil. In this study, the role of endosymbiont Piriformospora indica in counteracting salinity stress to Pakchoi plants was determined by studying physiological, biochemical, and molecular mechanisms. The physiological markers such as antioxidant enzymes, malondialdehyde (MDA), abscisic acid (ABA), salicylic acid (SA), ion analysis and electrolyte leakage as well as chlorophyll content were measured in pakchoi under two NaCl concentrations (100 and 200 mM) in inoculated and un-inoculated plants. In addition, the expression level of some well-known genes involved in Na+/K+homeostasis was also elucidated in different plant tissues. P. indica co-cultivation significantly increased biomass of Pakchoi as well as antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and augmented the level of Plant hormones (salicylic acid (SA)) and gibberellic acid (GA), assisting the plants to cope salinity stress. The salt tolerance mechanism of the experimental plant was studied at the cellular level by quantifying the gene expression level of salt overly sensitive (SOS) signaling pathway including, SOS1 and SOS2 as well as NHX-type Na+/H+ antiporter (NHX1) from the shoot and root samples. The gene expression analysis showed the higher expression level of the candidate genes in inoculated plants under the given salt concentration. In conclusion, the findings suggest that the symbiotic association of endosymbiont P. indica can help the plants to overcome the salinity stress.