The treatment of pharmaceutical wastewater is challenging as it contains multiple pollutants and complex in nature. The conventional treatment methods are insufficient and it is essential to adopt advanced techniques for effective treatment. This study investigates the simultaneous degradation of a mixture of pollutants -amoxicillin (AMX), acetaminophen (ACET), and ciprofloxacin (CIP) from an aqueous solution by ozonation. High-performance liquid chromatography and liquid chromatography-mass spectrometry equipped with electrospray ionization (LC-ESI-MS) were employed for analysis. The experiments were conducted by varying the operating conditions such as ozone dose (1–5 mg/L), pH (3–9) and time (0–25 min) respectively. The mixture of each pollutant (5 mg/L) was removed maximum at the optimum condition of ozone dose: 4 mg/L, pH-9 and reaction time was found to be within 5 min. The experimental results indicate that the ozonation has a higher degradation potential even though the aqueous solution contains multiple pollutants and the simultaneous degradation of AMX, ACET and CIP was found to be 98%, 98.5% and 99% respectively at 2 min. The mineralization of these compounds was observed at 89%. The degradation byproducts formed during the ozonation were identified using LC-ESI-MS. Further, the degradation mechanism and possible pathway of targeted pollutants were reported.