The current opioid epidemic remains an ongoing challenge, exacerbated by the extreme potency of synthetic opioids (e.g., fentanyl and fentanyl analogues), leading to an increase in adulterated heroin-related deaths. The increasing prevalence of fentanyl and fentanyl analogues in mixtures with heroin and other adulterants, excipients, and bulking agents has placed an emphasis on trace analysis methods for their detection from complex drug mixtures. Here, gradient elution moving boundary electrophoresis (GEMBE), a robust and miniaturized electrophoretic separation technique, was employed for the separation and detection of fentanyl and nine (9) fentanyl analogues from mixtures. GEMBE incorporated a short capillary (5 cm × 15 μm i.d.) for the electrophoretic separation of analytes with an opposing bulk counterflow. As the velocity of the counterflow was varied, analytes with differing electrophoretic mobilities entered the separation channel at different times and were analyzed as moving boundaries by contactless conductivity detection. The continuous injection of sample, driven by a controlled and variable pressure, both provided selectivity of the analytes and prevented contaminants or particulate within the sample from entering the separation capillary. Fentanyl was successfully separated and detected down to 2.5 μmol/L and demonstrated only 50% to 60% signal suppression in dilute binary mixtures with heroin and other common adulterants and excipients at 30:1 (compound/fentanyl) concentration ratios. In addition, GEMBE was successfully applied to a few adjudicated case samples of fentanyl-related mixtures exhibiting dyes and visible particulate. The short capillaries, contactless detection format utilized here, and continuous injection of sample allow for a small footprint platform that is easy-to-use for forensic analyses.