Abstract Background Methotrexate, an antifolate therapy, is used for the treatment of cancers, autoimmune disease, and transplant patients and needs to be carefully monitored for toxicity. Plasma measurement of methotrexate concentrations is problematic as a result of analytical interference of its metabolites. Immunoassays are widely used for monitoring therapeutic drug levels of methotrexate; however, chromatographic assays, LC-MS/MS most particularly, are preferentially used since they are less prone to metabolite interference. Methods Analytical performance was evaluated in a second-generation methotrexate immunoassay (ARK, Inc.) by testing precision, accuracy, linearity, interference, and method comparison with LC-MS/MS. Cross-reactivity of the immunoassay with 4-deoxy-4-amino-N10-methylpteroic acid (DAMPA), 7-OH methotrexate, and folic acid was also measured. Results Findings indicate that the within-run %CV ranged from 2.6% to 4.4% across control materials. The assay was linear across an analytical measuring range of 0.03 to 1.3 μM. The lower limit of the measuring interval and the lower limit of detection were established at 0.03 µM and 0.0067 μM, respectively. Notable interference from DAMPA was observed above 1 µM, whereas 7-OH methotrexate and folic acid showed no interference up to 5 µM and 1000 µM, respectively. Correlation studies showed an average 3% bias in DAMPA-free samples (R2 = 0.9935) and a significant bias and poorer correlation (R2 = 0.3241) in samples containing DAMPA. Conclusions The assay performed well based on the validation experiments and is suitable for most clinical applications involving methotrexate. However, the significant interference with DAMPA highlights the necessity for careful assay selection and interpretation of glucarpidase-treated patients.