Introduction The use of electronic cigarettes (ECs) is rapidly evolving as an alternative to traditional tobacco cigarettes. While ECs are likely less harmful than tobacco use, they are not considered completely harmless to human health. However, there is increasing evidence supporting their efficacy in smoking cessation. In our study, we investigated the presence of polycyclic aromatic hydrocarbon (PAH) biomarkers and their oxygenated and nitrated derivatives in the urine of tobacco smokers who switched to exclusive EC use for 28 days. Methods We employed the solid-phase microextraction (SPME) method to efficiently extract the targeted analytes and quantified them using gas chromatography mass spectrometry (GC-MS). High extraction efficiency and sensitivity was achieved by directly immersing the SPME PDMS/DVB fiber into diluted urine samples, incubated at 70°C for 30 min. A total of 100 urine samples were analyzed from 20 participants aged 20–68 years. Results In 80% of the analyzed samples, the concentrations of PAH biomarkers and their derivatives in participants' urine decreased by up to 90% after switching to EC. Two PAH biomarkers, 2-naphthol and 1-OH-pyrene, were quantified in 88 urine samples. Two oxygenated PAHs (1,4-naphthoquinone and 9-fluorenone) were quantified in 19 urine samples, while two nitrated PAHs (1-nitronaphthalene and 2-nitrofluorene) were quantified in 15 urine samples. The concentration of PAH biomarkers before and after switching to EC ranged 0.04–174.8 ng/mg creatinine and 0.1–115.8 ng/mg creatinine, respectively. PAH derivative concentrations in smokers ranged 0.1–26.4 ng/ mg creatinine, while after switching to EC, PAH derivative concentrations were mostly below the limit of detection and quantification. Conclusions EC consumers must be aware that using EC alone is not harmless. The presence of PAH derivatives in urine needs more assessment studies to understand both their mechanism of formation in the human body and risk to health.