Pistachio is a tree of the arid and semi-arid regions where salinity and boron (B) toxicity can be major environmental stresses. In this study, individual and combined effects of different concentrations of NaCl (0, 800, 1600, 2400 and 3200 mg kg−1 soil) and B (0, 2.5, 5.0, 10.0 and 20.0 mg kg−1 soil) were studied on growth, gas-exchange and mineral composition of pistachio seedlings for a duration of 120 days. Excess amounts of salinity (> 1600 mg NaCl kg−1 soil) and B (20.0 mg kg−1 soil) significantly reduced the plant growth and CO2 assimilation, which was associated with accumulation of Na, Cl and B in leaves. There was also a decline in cell membrane stability index (MSI). Reduced stomatal conductance (gs) was the primary cause of inhibition of photosynthesis rate (PN) under mild to moderate salinity. However, under severe salt stress and B toxicity, non-stomatal effects contributed to the inhibition of CO2 assimilation in addition to the decline in gs value. Application of 5.0–10.0 mg B kg−1 soil significantly improved the plant growth and PN and also recovered the MSI as countermeasures against salt stress. These observations were related to the role of B in cell membrane structure and functioning which reduced the concentration of toxic ions in the leaves. However, cell membrane damages and chlorophyll loss in plants affected by salt were observed to be exacerbated when excess amounts of B were present. In conclusion, the results revealed that optimizing the B nutrition can improve the performance of pistachio seedlings under salt stress, and NaCl also showed a mitigating effect on B toxicity if its concentration in the soil is kept under the plant salt tolerance threshold.