In order to increase the electrophoretic separation between fractions of analytes on a microfluidic chip, without the need for a longer separation channel, we propose and demonstrate a preparative electrokinetic procedure by which overlapping or closely spaced fractions are automatically split. The method involves an extra T-junction at the end of a separation channel and detector-triggered reconfiguration of voltages at channel outlets. Forced splitting of a separated four-component mixture is demonstrated, and possible sources of errors leading to contamination of split fractions are also discussed in detail and illustrated both by computational fluid dynamics and experiments. The splitting method can be applied in preparative CE-on-a-chip systems, for which it greatly simplifies downstream fraction manipulation and helps in reducing cross-contamination between collected fractions.