A stable and efficient surface-enhanced Raman scattering (SERS) substrate for neurotransmitter and cholinergic neurotransmission precursor detection was obtained by silver nanoparticle (AgNP) electrodeposition onto tin-doped indium oxide (ITO) using cyclic voltammetry. The size and surface coverage of the deposited AgNPs were controlled by changing the scan rate and the number of scans. The SERS performance of these substrates was analyzed by studying its reproducibility, repeatability and signal enhancement measured from p-aminothiophenol (p-ATP) covalently bonded to the substrate. We compared the SERS performance for samples with different Ag particle coverage and particle sizes. The performance was also compared with a commercial substrate. Our substrates exhibited a SERS enhancement factor of around 107 for p-ATP which is three orders of magnitude larger than for the commercial substrate. Apart from this high enhancement effect the substrate also shows extremely good reproducibility. The average spectral correlation coefficient (Γ) is 0.96. This is larger than for the commercial substrate (0.85) exhibiting a much lower SERS signal intensity. Finally, the application of our substrates as SERS bio-sensors was demonstrated with the detection of the neurotransmitters acetylcholine, dopamine, epinephrine and choline, the precursor for acetylcholine. The intensive SERS spectra observed for low concentrations of choline (2×10−6M), acetylcholine (4×10−6M), dopamine (1×10−7M) and epinephrine (7×10−4M) demonstrated the high sensitivity of our substrate. The high sensitivity and fast data acquisition make our substrates suitable for testing physiological samples.