A significant shift of migration time of nonretained compounds (ascorbic acid and cysteine) in micellar electrokinetic chromatography was observed under variation of sample matrix composition. The shift was affected by borate buffer concentration in sample matrix, sample injection time, and pH of BGE (80 mM SDS, Tris/HCl). Surprisingly, longer migration time of analyte was recorded at higher pH of separation buffer. These observations were linked to transient isotachophoresis process. Computer simulation with Simul5 software was conducted to support this hypothesis. The manuscript documents rarely reported in the literature phenomenon of isotachophoresis in micellar electrokinetic chromatography. The analytical potential of described observations was also discussed.