Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a nucleic acid amplification technique that utilizes the localized surface plasmon resonance effect of plasmonic nanomaterials under the irradiation of light with specific wavelengths to achieve rapid thermal cycling. PPT-PCR is considered as a next-generation PCR technique due to the potential to be applied to the development of point-of-care diagnostics and the fast, sensitive and accurate detection performance. In this study, we present PHANTOM, a proof-of-concept system that functionally integrates plasmonic photothermal PCR, magnetic nanoparticle removal, and swCNT-FET-based label-free electrical readout for rapid molecular diagnostics. The swCNT-FET sensor exhibits high sensitivity, capable of detecting low concentrations of target nucleic acids within minutes after PPT-PCR amplification. Besides, to improve the specificity of the assay, we introduce a hairpin structured primer to generate amplicons with an external single-strand tail that can hybridize with probes modified on the swCNT-FET sensor. With this design, an estimated limit of detection of 1.5 aM (experimentally validated down to 10 aM) was achieved within 20 min.