Single-component molecular conductors can provide a variety of electronic states. We demonstrate here that the Dirac electron system emerges in a single-component molecular conductor under high pressure. First-principles density functional theory calculations revealed that Dirac cones are formed in the single-component molecular conductor [Pd(dddt)2] (dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate), which shows temperature-independent resistivity (zero-gap behavior) at 12.6 GPa. The Dirac cone formation in [Pd(dddt)2] can be understood by a tight-binding model. The Dirac points originate from the HOMO and LUMO bands, each of which is associated with different molecular layers. Overlap of these two bands provides a closed intersection at the Fermi level (Fermi line) if there is no HOMO-LUMO coupling. Two-step HOMO-LUMO couplings remove the degeneracy on the Fermi line, resulting in gap formation. The Dirac cones emerge at the points where the Fermi line intersects with a line on which the HOMO-LUMO coupling is zero.