In this work, the performance of the atmospheric pressure chemical ionization (APCI) and photoionization (APPI) was assessed to develop a new selective and sensitive gas chromatography-high resolution mass spectrometry (GC-HRMS) method for the determination of polychlorinated naphthalenes (PCNs) in sediment samples. The capability of both APCI and APPI sources for the ionization of PCNs was investigated, showing the formation of the molecular ion and the [M‒Cl+O]‒ ion in positive and negative ion modes, respectively. Positive ion APCI provided high responses using high corona ion current, while the use of high vapour pressure dopant-solvents, such as toluene in positive mode and diethyl ether in the negative mode, was required to achieve high ionization efficiencies in APPI. The performance of the two API sources in the PCN determination by GC-HRMS were compared and the best results were achieved using the GC-APPI(+)-HRMS (Orbitrap) system. The GC-APPI(+)-HRMS (Orbitrap) method was applied to the characterization of Halowax mixtures and the analysis of marine sediments collected near to the coastal area of Barcelona (NE, Spain), demonstrating a great detection capability with low method limits of detection (0.2–1.6 pg g−1 dry weight), good precision (RSD <15%) and trueness (relative error <13%). Total PCN concentrations ranged from 0.35 to 5.0 ng g−1 dry weight and the presence of related compounds, such as polychlorinated biphenyls (PCBs), was also detected by combining positive and negative ion modes, providing complementary information to better monitor of all PCN congener groups. The results presented here show the feasibility of the GC-APPI-HRMS method for the suitable determination of PCNs.