Gastroesophageal reflux disease (GERD) is a highly prevalent condition. Screening for GERD remains a great challenge due to the non-specific nature of the symptoms. Now, salivary pepsin detection has become an effective tool for diagnosing GERD due to its non-invasive and highly specific advantages. However, the diagnosis of GERD by detecting pepsin in saliva still has factors such as long reaction time, poor selectivity, and low detection sensitivity, which need to be improved. In this work, bovine serum albumin (BSA) and a squaraine dye (SQ) were employed to build a BSA-SQ assembly with a fluorescent “on-off” change for rapid and sensitive detection of pepsin. In a Gly-HCl (pH = 2.6) buffer system, SQ had a significant aggregation caused-quenching (ACQ) effect. As SQ was embedded in the cavity of BSA, this improved its dispersion and inhibited the ACQ effect of SQ, resulting in enhanced fluorescence of the system. At this stage, pepsin catalyzed the hydrolysis of BSA, leading to the aggregation of SQ and the quenching of the fluorescence of BSA-SQ. The high catalytic activity of pepsin makes BSA-SQ suitable for the qualitative and quantitative detection of pepsin, showing a good linear relationship in the range of 0.5–40 μg/mL with a detection limit of 97 ng/mL. Finally, the use of this fluorescent probe method to detect pepsin in human saliva showed results consistent with conventional ELISA methods with relative errors between 0.4 and 5.5 %, confirming the great potential of BSA-SQ for the rapid diagnosis of GERD.