In this work, we present a new sensing approach for aqueous samples based on the microscope-FTIR spectrometer and applied for neurotransmitters. Our contribution in this work consists of a new sample handling system for the microscope-FTIR spectrometer based on a total reflective mirror, a heated hydrophobic layer for solvent removal/evaporation and sample confinement and a microfluidic system that handles sample injection unlike standard sample handling system which was based only on a total reflective mirror. In addition, another part of our contribution consists of proposing a new algorithm to extract molecular composition of the solution with high estimation ratios and based on the analysis of detected peaks on IR spectra. The data acquired from the microscope-FTIR spectrometer was analyzed by a newly developed algorithm to identify each neurotransmitter in homogeneous and non-homogeneous solutions with high selectivity. We used six neurotransmitter molecules (Dopamine hydrochloride, L-Ascorbic acid, Acetylcholine chloride, y-Aminobutyric, Glycine and L-Glutamic acid). The results obtained based on the algorithm developed showed that, using the new system, the six neurotransmitters can be identified in homogeneous and mixture solutions with an estimation ratio range of 88.8%-100% for Dopamine hydrochloride, 80%-100% for L-Ascorbic acid, 75%-100% for Acetylcholine chloride, 75%-100% for L-Glutamic, 77.7%-100% for y-Aminobutyric and 75%-100% for Glycine.