Background Limited information exists regarding the factor IX (FIX) coagulant activity (FIX:C) measured by different assays following FIX‐Padua gene therapy. Objective Assess for the first time FIX:C in five commonly used coagulation assays in plasma samples from hemophilia B subjects receiving FIX‐Padua gene transfer. Methods FIX:C was compared between central (n = 1) and local laboratories (n = 5) in the study, and across four commonly used FIX:C one‐stage assays and one FIX:C chromogenic assay. For comparison, samples of pooled congenital FIX‐deficient plasma spiked with purified recombinant human FIX (rHFIX)‐Padua protein or rHFIX (nonacog alfa) to obtain FIX:C concentrations from ~20% to ~40% were tested. Results FIX:C results at local laboratories strongly correlated with central laboratory results. However, absolute values at the central laboratory were consistently lower than those at local laboratories. Across five different FIX:C assays, a consistent pattern of FIX:C was observed for subjects receiving fidanacogene elaparvovec‐expressed gene transfer. Use of Actin FSL activated partial thromboplastin time (APTT) reagent in the central laboratory resulted in lower FIX:C values compared with other APTT reagents tested. The chromogenic assay determined lower FIX:C than any of the one‐stage assays. The rHFIX‐Padua protein–spiked samples showed similar results. In contrast, FIX:C results for rHFIX‐nonacog alfa measured within 25% of expected for all one‐stage assays and below 25% in the chromogenic assay. Conclusions Assay‐based differences in FIX:C were observed for fidanacogene elaparvovec transgene product and rHFIX‐Padua protein, suggesting the variable FIX:C determined with different assay reagents is inherent to the FIX‐Padua protein and is not specific to gene therapy–derived FIX‐Padua.