In order to adopt a general workflow for complex biological matrices with respect to a new blood–brain barrier (BBB) model, a micellar electrokinetic chromatography method has been developed. The cells forming the BBB have been cultivated in a special cell growth medium in which six drugs (acetaminophen, caffeine, carbamazepine, cimetidine, indometacin and propranolol) have been dissolved and tested for their penetration properties. The results showed good to very good accordance to the reference values. Samples were directly injected onto the capillary without any pretreatment (fused silica capillary, id: 50 μm, L: 48 cm, l: 40 cm). After method development, separations were carried out using a 60 mM borate buffer containing 200 mM of SDS at 30 kV, leading to an analysis time of less than 10 min. Between two runs the capillary was rinsed with a mixture of equal parts of running buffer and isopropanol (70% v/v), which proved to be very effective to remove matrix compounds. An appropriate choice of the detection wavelength (220 or 254 nm) could avoid major interferences between analytes and matrix. The typical RSD% for migration times was approximately 2%, for peak areas, it ranged from 2 to 6%, which was very well acceptable for the generic method used in this study and the low concentrations investigated. The LODs ranged from 10 to 30 ng/mL.