Our article presents the comparison of two methods: high-performance thin-layer chromatography (HPTLC) and pressurized planar electrochromatography (PPEC), implemented for the separation of a test mixture of purine derivatives. The two methods were compared in terms of separation selectivity and separation time. Our results show that PPEC enables the separation of the mixture (azathioprine, caffeine, theobromine, theophylline and acyclovir) which could not be efficiently separated in the HPTLC system, due to the different selectivities of separation. PPEC also enables to obtain a much faster separation, performed on the longer distance, in comparison to HPTLC. This makes PPEC a technique which can be useful in the analysis of purine derivatives and other drugs.