Lung cancer can be non-invasively detected by exhaling, which is why early detection is so important. Malignant growths in the lungs of an unwell person can be detected by analysing their breath profile. In this work, isoprene—a well-known lung cancer biomarker—is sensed using B40 as a molecular junction. An evaluation is conducted on the electronic transport properties of the molecular junction that has been constructed to detect isoprene. The extensive investigation is conducted to study the electronic properties i.e. density of states, transmission spectrum for the equilibrium condition and non-equilibrium conditions using density functional theory. Furthermore, the transport properties i.e. transmission eigenstates and current—voltage characteristics are analysed for isoprene-B40 molecular junction using non-equilibrium Green's function (NEGF) formalism. Upon investigation, it is revealed that the isoprene biomarker introduces improved transmission across the junction and hence increases the conductivity of the B40 molecular junction with isoprene present in the scattering region. Also, it is observed from the electronic properties analysis that the highest occupied molecular orbitals are the main contributors to the transmission in the B40-isoprene molecular junction. The transmission eigenstate analysis validates the transmission and shows the delocalized states responsible for conduction. The IV analysis is an indicative of the presence of negative-differential resistance behaviour in the junction which is useful for future device applications.