We previously proposed an evaluation method for detecting both respiration and heartbeat signals from the airflow at the mouth (Kawaoka et al 201518th Int. Conf. on Solid-State Sensors, Actuators and Microsystems; Kawaoka et al 2015 IEEE Sensors; Kawaoka et al 2016 Technical Digest IEEE Micro Electro Mechanical Systems Conf.). In the current study, we developed a catheter flow sensor with temperature compensation that uses MEMS technologies and used it to directly detect the breathing airflow in the airway of a rat. The temperature sensors were integrated with the catheter flow sensor. Heaters working as airflow and temperature sensors were produced on polymer film by using the same fabrication process so that the temperature coefficients of their resistances would coincide. As a result, the variation in sensor outputs due to the airflow temperature changes ranging from 20 °C to 34 °C was suppressed to less than 2.5%. The developed catheter flow sensor was inserted into the airway of a rat to detect both respiration and heartbeat signals. The accuracy of the breathing airflow measurements was improved thanks to the temperature compensation. The tidal volume variations between the expired and inspired air were suppressed to within 5%. Heartbeat signal information was extracted from the measured breathing waveforms by applying a discrete Fourier transform.