Silicon (Si) nutrition mediates many metabolic processes and stress responses. Here, we investigated the effect of Si on sodium (Na) transporters at the molecular level against salinity stress in apple plant. An apple plant (Malus domestica Borkh.) cv. ‘Fuji’ grafted onto MM106 clonal rootstock was chosen for the experiment. Up until the start of the experiment, all plants were irrigated with tap water, and 1 month later (in April) plants were watered with 35 mM NaCl solution. At 2 months following salt stress, three different calcium silicate (CaSiO3) doses (0.5, 1 and 2 mM) were applied twice at a 1-month interval (in June and July) to plant rhizosphere (roots) as solution, except control. Control plants were not treated with CaSiO3 and the plants were watered with NaCl solution. At 1 and 4 months following the salinity (short- and long-term salt stress, respectively), expression levels of SOS1 and NHX1 were determined. Under both short- and long-term salinity, expression levels of SOS1 and NHX1 genes increased compared to control. In summary, Si treatment may mitigate salt stress damage by mediating Na+ transport in Malus species.