Purpose Sarcopenia, characterized by loss of skeletal muscle mass (SMM) and strength, often leads to dysphagia in the elderly. This condition can also worsen treatment outcomes in head and neck cancer (HNC) patients, who are susceptible to swallowing difficulties. This study aimed to establish the correlation between swallowing muscle mass (SwMM) and SMM in HNC patients. Methods Data from 157 HNC patients in the OncoLifeS biobank of the University Medical Center Groningen were analyzed using pre-treatment neck CT scans. The SwMM was assessed by the cross-sectional area (CSA) of the tongue complex muscles (TCM), and SMM was indicated by the skeletal muscle index (SMI), calculated from corrected CSA at the third lumbar vertebra (L3). Correlations between SwMM and SMM were analyzed using Pearson or Spearman tests, and multivariable linear regression with SMI as dependent variable was performed. Results SwMM was moderately correlated with SMI (r = 0.600, p < 0.001), CSA at C3 (r = 0.538, p < 0.001), and CSA at L3 (r = 0.651, p < 0.001). The CSA at C3 strongly correlated with SMI (r = 0.871, p < 0.001). In multivariable regression analysis, age, sex, and weight were strong predictors of SMI, while the TCM area was a less robust predictor (p = 0.059). Models with CSA at C3 and L3 showed all variables as significant predictors (p < 0.001). Conclusions Although SwMM was significantly correlated with SMI and holds clinical utility, it is not strong enough to be considered interchangeably with C3 for predicting SMI, suggesting that swallowing muscles represent a different entity than skeletal muscles and not reflect accurately the general muscle mass.