The levels of persistent organic pollutants, polychlorinated biphenyls (PCBs), were determined in seawater and marine sediments from different sites along the Jordanian coast of the Gulf of Aqaba. Concentrations of 7 PCBs, namely, PCB-28, PCB-52, PCB-101, PCB-118, PCB-138, PCB-153, and PCB-180, were determined. An automated Soxhlet (Soxtec) extraction method was used for extraction with hexane–acetone as a solvent, and a pre-washed multilayer silica gel column was used for the clean-up step. Samples were analyzed using capillary gas chromatography (GC) with an electron capture detector (ECD) and GC–mass spectrometry (GC–MS) for confirmation. The method's limits of detection (LOD) were determined to be from 0.40 to 1.53 ng/L and from 0.39 to 0.91 ng/g dry weight for seawater and sediment, respectively. Concentrations of PCBs in seawater and sediment samples from all sites were below the LOD. This study provides evidence that very low concentrations of PCBs (<2 ng/g) were found in the water and sediments of the Jordanian coast of the Gulf of Aqaba. PCB concentrations measured in this study can be considered as a baseline for future monitoring and control of PCBs as requested by the Stockholm Convention.