In the present work, a sensitive and selective enzyme-linked electrochemical sensor technology using magnetic beads assay was demonstrated for voltammetric detection of microRNAs (miRNAs) as the first time herein by using the multi-channel screen-printed array of electrodes (MUX-SPE16s). The streptavidin coated magnetic beads were used as a solid phase to immobilize biotinylated DNA capture probe, and then the complementary target RNA sequence (miRNA-15a) was recognized with the capture DNA probe. After attachment of the streptavidin–alkaline phosphatase enzyme (SALP) to biotinylated hybrid, the electroactive product α-naphthol was measured +0.188 V by linear sweep voltammetry (LSV) technique in combination with a single-use pencil graphite electrode (PGE) compared to MUX-SPE16. The oxidation signal of α-naphthol indicates the hybridization occurred between DNA probe and its RNA target in the sample. The selectivity of our assay was tested in the presence of non-complementary miRNA sequence, a very good discrimination was achieved compared to the results obtained with the full match hybridization of probe with miRNA-15a target. The detection limit of miRNA-15a target sequence was also calculated as 0.992 μg/mL (98.60 pmole in 1 mL sample) at PGE, and 0.114 μg/mL (34.20 fmole in 3 μL sample) with MUX-SPE16 system.