Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label‐free detection of the nucleotides to determine their electrophoretic mobility (i.e., time‐of‐flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2‐deoxyribonucleoside 5'‐monophosphates, dNMPs, molecules in a label‐free manner by nanoscale electrophoresis. This is made possible by positioning two sub‐10 nm in‐plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label‐free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in‐plane nanopores and integrating different pre‐ and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication. A dual‐nanopore time‐of‐flight (TOF) sensor, which consists of two in‐plane nanopores formed at both ends of a nanochannel column, is designed and fabricated to determine the mobility of single molecules in nanoscale electrophoresis in a label‐free manner. This novel nanosensor with a 5 µm long nanochannel column demonstrates discrimination of four deoxynucleotide monophosphates (dNMPs) molecules with a mean identification accuracy of 94%.