A setup consisting of a bifurcated optical fiber made from high-transmission fused-silica cores with relatively high numerical apertures (NA=0.22), high-power cyan light-emitting diodes (LEDs) and Peltier cooling elements controlled by a proportional–integrative–derivative (PID) module is introduced to replace bulky, power- consuming lasers conventionally used in laser induced fluorescence (LIF) microchip capillary electrophoresis (μCE). The output fiber beam size, divergence, power distribution and power stability over time are documented. A modified epifluorescence microscope arrangement is used in conjunction with a compact fixed spectrometer aligned with a cooled charge-coupled device (CCD) camera for added sensitivity. Fluorescent dyes such as fluorescein, 6-carboxyfluorescein (6-FAM) and rhodamine B can be detected in cyclic olefin copolymer (COC) and glass microchannels at submicromolar levels. A single-stranded DNA oligonucleotide (10-mer) labeled with 6-FAM is also detected with reasonable signal-to-noise ratio when electrophoretically migrated at 100 V/cm. The compact LED excitation system presented herein will allow using capillary electrophoresis for DNA detection in compact mobile devices.