We preivously developed a catheter type flow sensor for measuring breathing and heartbeat information from breathing at the mouth [Hasegawa et al. J Micromech Microeng 27(12): 125016, (2017); Kawaoka et al. Tech. Dig. IEEE Micro Electro Mechanical Systems Conference 2016, pp 359–362]. In this study, we redesigned and developed the new sensor configuraiton for the catheter flow sensor to downsize and improve the sensor characteristics. The previous flow sensor consists of two pairs of a heater and a temperature compensation sensor for flow rate detection. The two heaters also functioned not only for flow rate detection but also for flow direction detection. The two temperature compensation sensors had a large footprint and corresponded to each heater. Therefore, the sensor occupied a large area, and it was necessary to match the heater characteristics for flow rate detection. The newly designed sensor is composed of a set of a heater and a temperature compensation sensor and two flow direction sensors. By providing the new flow direction sensors, the number of temperature compensation sensors with a large footprint was reduced to one. Thus, the area of the new sensor design was 15.0 mm2, which was reduced to 54.5% of the 27.0 mm2 of the previous sensor area by providing the flow direction sensors. Then, the new catheter type flow sensor was fabricated, and the flow characteristics for measuring breathing funciton were evaluated. Finally, we applied the catheter type flow sensor to an animal experiment using a rat, and it could evaluate the flow rate characteristics of the rat’s breathing as a reciprocating flow including flow direction. Moreover, the obtained breathing characteristics were within the range of the physiological values of rats.