A nanoscale interface between two immiscible electrolyte solutions (ITIES) provides a unique analytical platform for the detection of ionic species of biological interest such as neurotransmitters and neuromodulators, especially those that are otherwise difficult to detect directly on a carbon electrode without electrode modification. We report the detection of acetylcholine, serotonin, and tryptamine on nanopipet electrode probes with sizes ranging from a radius of ≈7 to 35 nm. The transfer of these analytes across a 1,2-dichloroethane/water interface was studied by cyclic voltammetry and amperometry. Well-defined sigmoidal voltammograms were observed on the nanopipet electrodes within the potential window of artificial seawater for acetylcholine and tryptamine. The half wave transfer potential, E1/2, of acetylcholine, tryptamine, and serotonin were found to be −0.11, −0.25, and −0.47 V vs E1/2,TEA (term is defined later in experimental), respectively. The detection was linear in the range of 0.25–6 mM for acetylcholine and of 0.5–10 mM for tryptamine in artificial seawater. Transfer of serotonin was linear in the range of 0.15–8 mM in LiCl solution. The limit of detection for serotonin in LiCl on a radius ≈21 nm nanopipet electrode was 77 μM, for acetylcholine on a radius ≈7 nm nanopipet electrode was 205 μM, and for tryptamine on a radius ≈19 nm nanopipet electrode was 86 μM. Nanopipet-supported ITIES probes have great potential to be used in nanometer spatial resolution measurements for the detection of neurotransmitters.