Purpose This prospective study was planned to investigate whether the combined isotonic technique of proprioceptive neuromuscular facilitation (PNF) is superior to Shaker exercises in improving the function of swallowing muscles. Methods Fifty individuals (30 females and 20 males; mean age 68 +/- 3.89 years) with swallowing difficulties were separated into two groups randomly. The treatment groups were Shaker and PNF groups, which performed these exercises three times in a week for6 weeks. Swallowing difficulties were determined with the Turkish version of the eating assessment tool (T-EAT-10). The 100 ml-water swallow test was used to measure capacity, volume, and speed of swallowing. Contraction amplitude changes used as a universal measurement of motor unit activity during the muscle action were measured with superficial electromyography. Result After 6 weeks of exercise training, T-EAT-10 scores decreased in both groups (p < 0.001). Water swallowing capacity and volume improved in both groups (p < 0.001). There was no change in swallowing speed in both groups (p > 0.05). Maximal voluntary contraction values of suprahyoid muscles were higher in PNF than the Shaker group (p < 0.05). Conclusion Both the types of exercise can be used in the rehabilitation of swallowing difficulties. However, the PNF technique increased the contraction amplitude values that occur during maximum contraction more than the Shaker exercises. Different functional evaluations are needed to determine the effectiveness of PNF on swallowing difficulty.