Cost-utility analyses (CUAs) increasingly use models to predict long-term outcomes and translate trial data to real-world settings. Model structure uncertainty affects these predictions. This study compares pharmacometric against traditional pharmacoeconomic model evaluations for CUAs of sunitinib in gastrointestinal stromal tumors (GIST). A two-arm trial comparing sunitinib 37.5 mg daily with no treatment was simulated using a pharmacometric-based pharmacoeconomic model framework. Overall, four existing models [time-to-event (TTE) and Markov models] were re-estimated to the survival data and linked to logistic regression models describing the toxicity data [neutropenia, thrombocytopenia, hypertension, fatigue, and hand-foot syndrome (HFS)] to create traditional pharmacoeconomic model frameworks. All five frameworks were used to simulate clinical outcomes and sunitinib treatment costs, including a therapeutic drug monitoring (TDM) scenario. The pharmacometric model framework predicted that sunitinib treatment costs an additional 142,756 euros per quality adjusted life year (QALY) compared with no treatment, with deviations - 21.2% (discrete Markov), - 15.1% (continuous Markov), + 7.2% (TTE Weibull), and + 39.6% (TTE exponential) from the traditional model frameworks. The pharmacometric framework captured the change in toxicity over treatment cycles (e.g., increased HFS incidence until cycle 4 with a decrease thereafter), a pattern not observed in the pharmacoeconomic frameworks (e.g., stable HFS incidence over all treatment cycles). Furthermore, the pharmacoeconomic frameworks excessively forecasted the percentage of patients encountering subtherapeutic concentrations of sunitinib over the course of time (pharmacoeconomic: 24.6% at cycle 2 to 98.7% at cycle 16, versus pharmacometric: 13.7% at cycle 2 to 34.1% at cycle 16). Model structure significantly influences CUA predictions. The pharmacometric-based model framework more closely represented real-world toxicity trends and drug exposure changes. The relevance of these findings depends on the specific question a CUA seeks to address.