To evaluate intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) and dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) sequences for quantitative characterization of anal fistula activity. This retrospective study was approved by the institutional review board. One hundred and two patients underwent MRI for clinical suspicion of anal fistula. Forty-three patients with demonstrable anal fistulas met the inclusion criteria. Quantitative analysis included measurement of DCE and IVIM parameters. The reference standard was clinical activity based on medical records. Statistical analyses included Bayesian analysis with Markov Chain Monte Carlo, multivariable logistic regression, and receiver operating characteristic analyses. Brevity of enhancement, defined as the time difference between the wash-in and wash-out, was longer in active than inactive fistulas (p = 0.02). Regression coefficients of multivariable logistic regression analysis revealed that brevity of enhancement increased and normalized perfusion area under curve decreased with presence of active fistulas (p = 0.03 and p = 0.04, respectively). By cross-validation, a logistic regression model that included quantitative perfusion parameters (DCE and IVIM) performed significantly better than IVIM only (p < 0.001). Area under the curves for distinguishing patients with active from those with inactive fistulas were 0.669 (95% confidence interval CI: 0.500, 0.838) for a model with IVIM only, 0.860 (95% CI: 0.742, 0.977) for a model with IVIM and brevity of enhancement, and 0.921 (95% CI: 0.846, 0.997) for a model with IVIM and all DCE parameters. The inclusion of brevity of enhancement measured by DCE-MRI improved assessment of anal fistula activity over IVIM-DWI only.