Profens are important non‐steroidal anti‐inflammatory pharmaceutical drugs and their behavior depends on their enantiomeric form. Three of the most employed profens, ketoprofen, naproxen and ibuprofen, were separated simultaneously in pairs by two‐dimensional achiral‐chiral high‐performance liquid chromatography using heart‐cut mode. The total amount of each profen was determined using a C8 column in the first achiral system; in the second chiral system, the enantiomeric fraction of each profen was determined using an α1‐acid glycoprotein column. Mobile phases were optimized by factorial design, response surfaces and multi‐response analysis paying particular attention to mobile phase compatibility of both columns and to transferring time between systems. The effect of temperature on each profen and their enantiomer retention was studied, the thermodynamic parameters being calculated. Calibration graphs were linear in the ranges of 2–20, 0.5–10 and 10–40 mg/L for ketoprofen, naproxen and ibuprofen respectively in both systems. The method allowed the analysis of three pharmaceuticals establishing the enantiomeric fraction of each profen using a simple sample preparation; moreover, the first achiral system cleans the sample deeply preventing deterioration of the expensive chiral column. Recoveries over 80% and the enantiomeric fraction of each profen were obtained allowing determination of the pharmaceutical purity.