Salinity is an abiotic stress that reduces the seed germination and productivity of tomatoes. Magnetic treatment has been shown to have a positive effect on the seed germination, seedling growth, and productivity of various crop species. Therefore, three experiments were conducted to evaluate whether treating saline water or seeds with a magnetic field can improve the seed germination and productivity of tomatoes (Solanum lycopersicum) under salinity stress. To evaluate seed germination and seedling growth in response to a magnetic field, two laboratory experiments were carried out by passing four saline water solutions of NaCl (0, 5, 10, and 15 dS/m) through a magnetic field (3.5–136 mT) or exposing tomato seeds to the same magnetic field for 20 min before sowing. In a greenhouse experiment, plants were irrigated with different magnetically-treated and untreated saline water solutions to evaluate plant growth. Magnetic treatment of water or seeds improved seed germination percentage, speed of germination (lower mean time to germination), and seedling length and dry weight in the two laboratory experiments, especially under salinity stress of 5 and 10 dS/m. As the salinity level increased, germination performance and plant growth were significantly decreased. Irrigating tomato plants with magnetically-treated water improved plant height, stem diameter, and fruit yield per plant compared to untreated water, especially under salinity of 0 and 5 dS/m. In conclusion, magnetic treatment of saline water or seeds improved germination performance, plant growth, and fruit yield of tomatoes under saline conditions.