IntroductionFor the analysis of clinical effects, multiple imputation (MI) of missing data were shown to be unnecessary when using longitudinal linear mixed-models (LLM). It remains unclear whether this also applies to trial-based economic evaluations. Therefore, this study aimed to assess whether MI is required prior to LLM when analyzing longitudinal cost and effect data.MethodsTwo-thousand complete datasets were simulated containing five time points. Incomplete datasets were generated with 10, 25, and 50% missing data in follow-up costs and effects, assuming a Missing At Random (MAR) mechanism. Six different strategies were compared using empirical bias (EB), root-mean-squared error (RMSE), and coverage rate (CR). These strategies were: LLM alone (LLM) and MI with LLM (MI-LLM), and, as reference strategies, mean imputation with LLM (M-LLM), seemingly unrelated regression alone (SUR-CCA), MI with SUR (MI-SUR), and mean imputation with SUR (M-SUR).ResultsFor costs and effects, LLM, MI-LLM, and MI-SUR performed better than M-LLM, SUR-CCA, and M-SUR, with smaller EBs and RMSEs as well as CRs closers to nominal levels. However, even though LLM, MI-LLM and MI-SUR performed equally well for effects, MI-LLM and MI-SUR were found to perform better than LLM for costs at 10 and 25% missing data. At 50% missing data, all strategies resulted in relatively high EBs and RMSEs for costs.ConclusionLLM should be combined with MI when analyzing trial-based economic evaluation data. MI-SUR is more efficient and can also be used, but then an average intervention effect over time cannot be estimated.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10198-022-01525-y.