Due to their small size and unique properties, single-molecule electronics have long seen research interest from experimentalists and theoreticians alike. From a theoretical standpoint, modeling these systems using electronic structure theory can be difficult due to the importance of electron correlation in the determination of molecular properties, and this electron correlation can be computationally expensive to consider, particularly multiconfigurational correlation energy. In this work, we develop a new approach for the study of single-molecule electronic systems, denoted NEGF-MCPDFT, which combines multiconfiguration pair-density functional theory (MCPDFT) with the non-equilibrium Green’s function formalism (NEGF). The use of MCPDFT with NEGF allows for the efficient inclusion of both static and dynamic electron correlations in the description of the junction’s electronic structure. Complete active space self-consistent field wave functions are used as references in the MCPDFT calculation, and as with any active space method, effort must be made to determine the proper orbital character to include in the active space. We perform conductance and transmission calculations on a series of alkanes (predominantly single-configurational character) and benzyne (multiconfigurational character), exploring the role that active space selection has on the computed results. For the alkane junctions explored (where dynamic electron correlation dominates), the MCPDFT-NEGF results agree well with the DFT-NEGF results. For the benzyne junction (which has a significant static correlation), we see clear differences in the MCPDFT-NEGF and DFT-NEGF results and evidence that NEGF-MCPDFT is capturing additional electron correlation effects beyond those provided by the Perdew–Burke–Ernzerhof functional.