The fabrication and application of a electrochemical detector (ED) with the thioctic acid (TA)/iridium oxide (IrO2)–palladium (Pd) chemically modified electrode (CME) for liquid chromatography (LC) were described. The electrochemical behavior of dopamine (DA) and ascorbic acid (AA) at the TA/IrO2–Pd CME were investigated by differential pulse voltammetry (DPV). It was found that the CME could be permselective to DA cations and exile the AA anions, which could be used to determine the monoamine neurotransmitters and avoid the interference of AA in LC. In liquid chromatography with electrochemical detection (LC–ED), DA, norepinephrine (NE), 5-hydroxytryptamine (5-HT), epinephrine (E) and 3,4-dihydroxyphenylactic acid (DOPAC) were determined at the CME. The linear ranges of five analytes were over three orders magnitude and the limits of detection were 0.05 pmol for DA, 0.05 pmol for NE, 0.05 pmol for E, 0.10 pmol for 5-HT and 1.00 pmol for DOPAC. The application of this method coupled with microdialysis sampling for the in vivo determination of the monoamines in rat brain was also investigated.