An electromagnetic flowmeter (EMFM) has been used in the main cooling loop of the fast reactor, but the large-sized magnet structure of conventional EMFMs was not adopted. Therefore, it is necessary to develop a novel EMFM with small-sized magnets for the fast reactor. But the fear is that the decrease in the magnetic field and the end effect will make the EMFM’s performance worse, though there is no detailed information about the end effect due to such small-sized magnets. This paper describes the EMFM with small-sized magnets for coolant monitoring. By using three-dimensional steady-state electromagnetic analysis, we have studied numerically the end effect of an EMFM with saddle-shaped permanent magnets that are smaller in size than the pipe diameter. Consequently, it has been clarified that the performance of an EMFM can be improved by utilizing the effect of the downstream end of magnets and by combining the inclined electrodes and the effect of the circumferential ends of magnets.