A recently reported chiral strong cation exchanger (cSCX) type stationary phase was investigated for the LC separation of a series of Cinchona alkaloids and synthetic derivatives thereof to test its usefulness as alternative methodology for the separation of those important pharmaceuticals. The cSCX column-packing material was qualitatively compared on the one hand against a commercially available non-enantioselective SCX-material, PolySulfoethyl-A, and, on the other hand, against a modern C18 reversed-phase stationary phase which is commonly employed for Cinchona alkaloid analysis. Both SCX columns showed no pronounced peak-tailing phenomena which typically hamper Cinchona alkaloid RP analysis and require specific optimization. Thus, the cSCX-based assay provided new feasibilities for the separation of the Cinchona alkaloids in polar organic mode as opposed to conventional reversed-phase methodologies. In particular, a method for the simultaneous determination of eight Cinchona alkaloids (quinine, quinidine, cinchonine, cinchonidine, and their corresponding dihydro analogs) using the cSCX column in HPLC has been developed and exemplarily applied to impurity profiling of a commercial alkaloid sample. Furthermore, both SCX materials allowed successful separation of C9-epi and 10,11-didehydro derivatives from their respective educts in an application in synthetic Cinchona alkaloid chemistry.