Detecting complete viral particles in vaccines is essential for both monitoring vaccine production and ensuring vaccine quality. Currently, sucrose density gradient centrifugation is the standard method for measuring the antigen content in conventional inactivated vaccines, but it requires specialized equipment and skilled personnel. Recently, BODIPY (BDP) dyes have gained attention in biomolecular studies due to their modifiable parent structure, although their use in macromolecular proteins remains limited. This study successfully synthesized a fluorescent antibody, BDP-VHH (variable domain of a heavy chain of a heavy chain-only antibody), through the nucleophilic substitution of BDP-2Cl with VHH, which recognizes the 146S antigen of the foot-and-mouth disease virus (FMDV). We investigated its use in quantifying FMDV serotype O antigen and cell imaging. The results showed that the BDP-VHH-based method can quantify the antigen within 1 h with good repeatability and sensitivity. Compared with FITC-conjugated antibodies, BDP-VHH demonstrated improved light stability. This study provides a foundation for the use of BDP fluorescent dyes in the macromolecular biological research.