A cross validation analysis evaluating computer model prediction accuracy for a priori planning magnetic resonance-guided laser induced thermal therapy (MRgLITT) procedures in treating focal diseased brain tissue is presented. Two mathematical models are considered. (1) A spectral element discretization of the transient Pennes bioheat transfer equation is implemented to predict the laser induced heating in perfused tissue. (2) A closed-form algorithm for predicting the steady state heat transfer from a linear superposition of analytic point source heating functions is also considered. Prediction accuracy is retrospectively evaluated via leave-one-out cross validation (LOOCV). Modeling predictions are quantitatively evaluated in terms of a Dice similarity coefficient (DSC) between the simulated thermal dose and thermal dose information contained within N = 22 MR thermometry datasets. During LOOCV analysis, the transient model’s DSC mean and median is 0.7323 and 0.8001, respectively, with 15 of 22 DSC values exceeding the success criterion of DSC ≥ 0.7. The steady state model’s DSC mean and median is 0.6431 and 0.6770, respectively, with 10 of 22 passing. A one-sample, one-sided Wilcoxon signed rank test indicates that the transient FEM model achieves the prediction success critera, DSC ≥ 0.7, at a statistically significant level.