Herein, a fabric phase sorptive extraction-based scheme was reported for the determination of amphotericin B in human urine. The developed method allowed the direct extraction of the analyte from the biological matrix with improved selectivity, repeatability and recovery. Due to the membrane’s engineered affinity towards the analyte, extraction equilibrium was achieved in 30 min. Moreover, no additional sample pretreatment was required due to the high permeability of the FPSE membrane and the small volume of eluting solvent required for quantitative back-extraction of the analytes. The hydrophobic sol–gel polydimethylphenylsiloxane (sol–gel PDMDPheS) coated membrane provided the optimum extraction performance. Important parameters that affect the extraction efficiency (such as sample volume, extraction time, membrane size, stirring rate, ion strength, elution solvent and time) were thoroughly investigated. The analyte was separated from the internal standard (nimesulide) and endogenous compounds of the human urine using a gradient elution program. The proposed assay was linear within the range of 0.10–10.0 μg mL−1 while the relative standard deviation of the repeatability (sr) and within-laboratory reproducibility (sR) were less than 12.7% in all cases. The method exhibited good accuracy which varied between 88.1 to 110.3%. The developed method was successfully applied for the monitoring of amphotericin B concentration in human urine.