Abstract Objective. To provide an open-source software for repeatable and efficient quantification of T ₁ and T ₂ relaxation times with the ISMRM/NIST system phantom. Quantitative magnetic resonance imaging (qMRI) biomarkers have the potential to improve disease detection, staging and monitoring of treatment response. Reference objects, such as the system phantom, play a major role in translating qMRI methods into the clinic. The currently available open-source software for ISMRM/NIST system phantom analysis, Phantom Viewer (PV), includes manual steps that are subject to variability. Approach. We developed the Magnetic Resonance BIomarker Assessment Software (MR-BIAS) to automatically extract system phantom relaxation times. The inter-observer variability (IOV) and time efficiency of MR-BIAS and PV was observed in six volunteers analysing three phantom datasets. The IOV was measured with the coefficient of variation (CV) of percent bias (%bias) in T ₁ and T ₂ with respect to NMR reference values. The accuracy of MR-BIAS was compared to a custom script from a published study of twelve phantom datasets. This included comparison of overall bias and %bias for variable inversion recovery (T ₁ ^VIR), variable flip angle (T ₁ ^VFA) and multiple spin-echo (T ₂ ^MSE) relaxation models. Main results. MR-BIAS had a lower mean CV with T ₁ ^VIR (0.03%) and T ₂ ^MSE (0.05%) in comparison to PV with T ₁ ^VIR (1.28%) and T ₂ ^MSE (4.55%). The mean analysis duration was 9.7 times faster for MR-BIAS (0.8 min) than PV (7.6 min). There was no statistically significant difference in the overall bias, or the %bias for the majority of ROIs, as calculated by MR-BIAS or the custom script for all models. Significance. MR-BIAS has demonstrated repeatable and efficient analysis of the ISMRM/NIST system phantom, with comparable accuracy to previous studies. The software is freely available to the MRI community, providing a framework to automate required analysis tasks, with the flexibility to explore open questions and accelerate biomarker research.