There are few studies to date that determine the effects of ibuprofen on mitochondrial membrane potential (ΔΨM) and DNA integrity in neotropical fish. The objective of this study is to determine if four months’ exposure to ibuprofen in different concentrations (25 and 50 µg/L) produces effects on ΔΨM and alters the integrity of DNA in striped catfish Pseudoplatystoma magdaleniatum. For this study, the fish were placed in tanks with water at constant concentrations of 0 (control), 25, and 50 µg/L of ibuprofen for four months. Subsequently, blood samples were taken for analysis of ΔΨM and DNA integrity, using a flow cytometer LSRFortessa BD Biosciences. After four months of exposure to ibuprofen at different concentrations, the results showed no increase in Low ΔΨM, indicating that there are no alterations in the mitochondrial membrane potential. On the other hand, the percentages of DNA damage were below 0.39, which indicates that there were no alterations in DNA integrity. It is possible that under the conditions in which this study was conducted (ibuprofen levels, exposure time), they are not sufficient to demonstrate the effects caused by this drug. Higher ibuprofen levels and/or longer exposures may be required to determine alteration in ΔΨM and DNA integrity. Flow cytometric analysis for these types of samples is a fast, specific, and reliable technique, compared to traditional methods.