A flow-electrolytic cell that consists of a bare gold wire or of different thiol-compound-modified gold electrodes (such as 2,4-thiazolidinedione, 2-mercapto-5-thiazoline, 2-mercaptothiazoline, l-cysteine, thioglycolic acid) was designed to be used in a voltammetric detector to identify l-selenomethionine and Se-methylseleno-l-cysteine using high-performance liquid chromatography. Both l-selenomethionine and Se-methylseleno-l-cysteine are more efficiently electrochemically oxidized on a thiol/gold than on a bare gold electrode. For the DC mode, and for measurements with suitable experimental parameters, a linear concentration from 10 to 1600 ng·mL−1 was found. The limits of quantification for l-selenomethionine and Se-methylseleno-l-cysteine were below 10 ng·mL−1. The method can be applied to the quantitative determination of l-selenomethionine and Se-methylseleno-l-cysteine in commercial selenium-containing supplement products. Findings using high-performance liquid chromatography with a flow-through voltammetric detector and ultraviolet detector are comparable.