Inter-regional patient mobility represents both a resource and a challenge for the organization and financing of health systems, particularly in decentralised countries. We use cross-sectional time series regression analysis to test the determinants of imbalances in regional funds to finance inter-regional patient mobility for the 17 Spanish regions for the period 2014-2020. The findings indicate that highly specialised health centres and bilateral agreements partly explain the budget imbalance from inter-regional patient referrals, while local tourism partly explains the budget imbalance from non-referred patient mobility. Developing effective national schemes to compensate net patient recipient regions would be fundamental to addressing territorial imbalances.