There is great interest in using microfluidic channels packed with a stationary phase for chemical separations of complex mixtures. A key advantage of such techniques is the use of electroosmotic flow (EOF), controlled simply by applying electrical potentials between reservoirs. A disadvantage for this technique, however, is a lack of compatibility with gradient elution separations. This limitation arises from the dependence of EOF velocity on run buffer content (including the concentration of organic modifier). Here, we introduce a method for implementing gradient elution in electrochromatography in which multiple run buffers are velocity-matched, such that the elution profile resembles that found in conventional HPLC. This method is driven entirely with EOF, meaning that pumps, valves, and pressure fittings are not required. The method was validated by application to separations of peptide standards and protein digests. These results suggest that microfluidic electrochromatography may be compatible with a wide range of applications that have previously been unexplored.