Endotoxin is a lipopolysaccharide (LPS) that is found in the outer membrane of the cell wall of Gram-negative bacteria. Due to its high toxicity, the allowable endotoxin limit for water for injection is set at a very low value. Conventional methods for endotoxin detection are time-consuming and expensive and have low reproducibility. A previous study has shown that dipicolylamine (dpa)-modified pyrene-based probes exhibit fluorescence enhancement in response to LPS; however, the application of such probes to the sensing of LPS is not discussed. Against this backdrop, we have developed a simple and rapid endotoxin detection method using a dpa-modified pyrenyl probe having a zinc(II) center (Zn-dpa-C4Py). When LPS was added into Zn-dpa-C4Py solution, excimer emission of the pyrene moiety emerged at 470 nm. This probe can detect picomolar concentrations of LPS (limit of detection = 41 pM). The high sensitivity of the probe is ascribed to the electrostatic and hydrophobic interactions between the probe and LPS, which result in the dimer formation of the pyrene moieties. We also found that Zn-dpa-C4Py has the highest selectivity for LPS compared with other phosphate derivatives, which is probably caused by the co-aggregation of the probe with LPS. We propose that Zn-dpa-C4Py is a promising chemical sensor for the detection of endotoxin in medical and pharmaceutical applications.