Although the evaluation of the uncertainty of an analytical method is a mandatory step in the method's validation, its applicability to the monitoring of trace compounds in complex samples is not simple, nor is it part of the routine of most laboratories, namely those dedicated to research. This manuscript focuses on the full validation of an analytical procedure for determining trace concentrations of twenty-four pharmaceutical active compounds (PhACs) in wastewaters using solid-phase extraction (SPE) and ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The method optimization was performed on different wastewater matrices, namely influents and final effluents from two distinct wastewater treatment plants (WWTPs). Matrix effects and extraction efficiency (absolute recovery) of the developed method were determined. Validation was performed to obtain the method's linearity/working range, precision, trueness, method detection limits (MDLs) and method quantification limits (MQLs). The expanded uncertainty of the data obtained was estimated according to the requirements of international procedures dedicated to the expression of uncertainty. Different approaches for the estimation of uncertainty were applied. The validated method was used in the analysis of target PhACs in wastewater samples collected at two WWTPs. The obtained results facilitated the introduction of a validated method for routine measurement of PhACs in wastewater samples and allowed method accreditation by the competent national authority.