This study numerically investigated the flow characteristics in a rectangular enclosure filled with oil-based ferrofluid (EFH-1, Ferrotec.) under the influence of external magnetic fields. The rectangular enclosure contained obstacles with different shapes, such as a rectangle and a triangle mounted on the top and bottom wall surfaces. In order to generate external magnetic fields, a permanent magnet was located in the lower part of the rectangular enclosure, and its direction was selected to be either horizontal or vertical. Our results showed that the ferrofluid flow fields were affected by the applied external magnetic field direction and eddy flow phenomena in the working fluid were generated in the vicinity of high magnetic flux density distributions, such as at the edge of the permanent magnet. It was also confirmed that the magnetophoretic force distributions in the analysis model played a significant role in the development of the ferrofluid flow fields.