A flow cell incorporating a liquid junction was fabricated for sequential analysis using the surface-polarity-controlled sensor. In the present flow cell, a porous wall or an S-shaped route acts as a liquid junction to prevent contamination of the reference-electrode solution. The stability of the electric potential of the Ag/AgCl reference electrode in these flow-cell systems was studied, and both of the liquid junctions were highly effective in keeping the electrode potential stable. In the surface-polarity-control method, good agreement of sensor response was confirmed between the batch system and the flow-cell system with the S-shaped junction, although large resistance of the porous wall junction influenced the estimation of the impedance of the working electrode/solution interface. A portable and general-purpose chemical sensor can possibly be realized using the surface-polarity-controlled sensor with a flow-cell system which utilizes flow injection analysis.