The investigation of the ocular permeability and/or distribution of pranoprofen (PF), a non-steroidal antiinflamatory drug, demands for the selective analysis of its transit through specific ocular membranes. Therefore, customised ex vivo permeation experiments through external ocular tissues (cornea and sclera) have been validated for this drug in addition to its HPLC-UV quantification following standard bioanalytical guidelines. Chromatographic conditions consist of an isocratic system to elute the drug with a C18 column with UV detection at 245 nm. Precision, expressed as the relative standard deviation (% RSD), ranged between 4.89 and 0.79% (intra-day) and between 9.02 and 2.14% (interday). Accuracy ranged between 5.15 and -1.92% in intra-day experiments and between 6.25 and −4.89% in inter-day experiments. Drug recovery from tissue samples was reproducible around 90% and considered satisfactory to adequately assess drug levels in target tissues. Results indicate that the procedure is valid for the quantitation of PF in those ophthalmic samples in the range of 6.5 μg/mL to 100 μg/ml. As a proof of concept, PF permeation profiles through porcine cornea and sclera with vertical diffusion cells have been generated and analyzed. Pilot experiments demonstrate its applicability to investigate permeation levels of PF from 22.31 μg/cm2 (about a 20% of the dose) until 500 μg/cm2 if required. Additionally, real tissue-retention samples were also generated to verify the goodness of this experimental setup.