Fentanyl has become pervasive as a drug of abuse and as adulterant in seized drugs. Positional isomers analyzed by gas chromatography with mass spectrometry can follow the same fragmentation pathway and therefore may not be differentiated. Additionally, electron ionization leads to lack of discernible molecular ion for most fentanyl related compounds. Liquid chromatography may be used as an orthogonal identification technique with diode array ultraviolet and mass spectrometric detection. Here we provide a chromatographic method for the separation of 20 different fentanyl analogues, homologues and positional isomers using ultra high performance liquid chromatography with photodiode array ultraviolet and mass spectrometry detection. Five different columns were investigated utilizing reverse phase chromatography and hydrophilic interaction chromatography. Chromatographic systems were evaluated to determine which could separate the most compounds overall, as well as the most positional isomers. We found that isocratic elution, with a methanol modifier (35%) and formic acid (0.1%) as an additive, on a C18 column at a temperature of 25°C could resolve 10/20 compounds overall and 16/20 positional isomers. Using electrospray ionization, compounds with different masses could easily be distinguished based on their pseudo molecular ions. Ultraviolet detection facilitated differentiation of positional isomers that could not be distinguished by either electron ionization or electrospray ionization mass spectrometry alone.