In this study, the vertically-oriented pulsating heat pipe (PHP) heat exchangers charged with either water or HFE-7000 in a filling ratio of 35% or 50% were fabricated to exchange the thermal energy between two air streams in a parallel-flow arrangement. Both the effectiveness of the heat exchangers and the thermal resistance of PHP with a size of 132 × 44 × 200 mm, at a specific evaporator temperature ranging from 55 to 100 °C and a specific airflow velocity ranging from 0.5 to 2.0 m/s were estimated. The results show that the heat pipe charged with HFE-7000 in either filling ratio is likely to function as an interconnected array of thermosiphon under all tested conditions because of the unfavorable tube inner diameter, whereas the water-charged PHP possibly creates the pulsating movement of the liquid and vapor slugs once the evaporator temperature is high enough, especially in a filling ratio of 50%. The degradation in the thermal performance of the HFE-7000-charged PHP heat exchanger resulted from the non-condensable gas in the tube became diminished as the evaporator temperature was increased. By examining the effectiveness of the present heat exchangers, it is suggested that water is a suitable working fluid while employing the PHP heat exchanger at an evaporator temperature higher than 70 °C. On the other hand, HFE-7000 is applicable to the PHP used at an evaporator temperature lower than 70 °C.