Autoimmune factor XIII (FXIII) deficiency (AiF13D) is a rare hemorrhagic disease. The anti-FXIII autoantibodies that cause this disease are classified into three types: type Aa inhibits the heterotetramer assembly and activation of FXIII, type Ab inhibits the enzymatic activity of activated FXIII, and type B enhances the elimination of FXIII from the blood. The former two are FXIII inhibitors and may be lethal if overlooked by conventional functional assays. To reliably detect both types of FXIII inhibitors, a new assay was developed by incorporating 5-(biotinamido)pentylamine (BAPA) into α2-plasmin inhibitor (PI-BAPA assay). This assay was tested on plasma samples from 128 participants, including 60 healthy controls, 35 patients with non-immune acquired FXIII deficiency, and 33 patients with AiF13D (29 with type Aa inhibitors and 4 with type Ab inhibitors). The PI-BAPA assay successfully detected type Aa and Ab inhibitors in 5-step dilution cross-mixing tests between patient and normal plasma. This assay also showed comparable or superior inhibition rates in the 1:1 mixing test compared to conventional ammonia release and amine incorporation assays. Receiver operating characteristic curve analysis confirmed the excellent specificity and sensitivity of this assay for determining inhibition rates, and the assay has already been used for AiF13D diagnosis.