Inflammation is a vital protective response in living systems and closely related to various diseases. As a member of the reactive oxygen species (ROS) family, peroxynitrite (ONOO−) is involved in the organism’s inflammatory process and considered as an important biomarker of inflammation. Therefore, the construction of a simple, rapid, and sensitive tool for detecting ONOO− is of great importance for the diagnosis of inflammation. In this study, we constructed the new near-infrared fluorescence probe BDP-ENE-S-Py+ based on BODIPY dye, which has the advantages of fast response speed (2 min), good selectivity, and a high signal-to-noise ratio. Moreover, the probe had a good linear relationship (LOD = 120 nM) when the ONOO− concentration was 10–35 µM. In addition, BDP-ENE-S-Py+ could detect exogenous ONOO− in liver cancer cells without interference from other reactive oxygen species and visualize the fluctuations in ONOO− concentrations in cells. More importantly, BDP-ENE-S-Py+ was able to track the upregulation of ONOO− content in a mouse model of peritonitis induced by LPS. This work demonstrated that the near-infrared fluorescent probe for visualizing ONOO− level fluctuations could provide a promising tool for inflammation-related studies.