On the basis of the competition assay approach and fluorescent 11-mercaptoundecanoic acid-capped AuNCs (AuNCs@11-MUA) with unique optical properties, a convenient, reliable and highly sensitive real-time assay of pyrophosphatase (PPase) activity is established and developed for the first time. Pyrophosphate (PPi) could recover the Cu(2+)-quenched AuNCs@11-MUA fluorescence selectively owing to the higher binding affinity between PPi and Cu(2+) than that between 11-MUA and Cu(2+). Whereas PPase could catalyze the hydrolysis of PPi, thus released Cu(2+), leading to fluorescence requenching of the AuNCs@11-MUA. In the assay, a good linearity between the fluorescence response and PPase activity within a range from 1 to 20 mU is found, with a detection limit of less than 1 mU, which is better than other PPase assays using PPi as the substrate. Additionally, we demonstrate that our AuNCs@11-MUA-based fluorescent assay can be applied to assay the PPase activity in real biological samples such as the cell lysate. This strategy paves a new avenue for exploring the sensing applications of fluorescence AuNCs and improving the development of competition assay approach.