Capturing the vertical profiles and horizontal variations of atmospheric aerosols often requires accurate airborne measurements. With the advantage of avoiding health and safety concerns related to the use of butanol or other chemicals, water-based condensation particle counters have emerged to provide measurements under various environments. However, airborne deployments are relatively rare due to the lack of instrument characterization under reduced pressure at flight altitudes. This study investigates the performance of a commercial “versatile” water-based condensation particle counter (vWCPC, model 3789, TSI, Shoreview, MN, USA) under various ambient pressure conditions (500–920 hPa) with a wide range of particle total number concentrations (1500–70 000 cm−3). The effect of conditioner temperature on vWCPC 3789 performance at low pressure is examined through numerical simulation and laboratory experiments. We show that the default instrument temperature setting of 30 ∘C for the conditioner is not suitable for airborne measurement and that the optimal conditioner temperature for low-pressure operation is 27∘. Under the optimal conditioner temperature (27∘), the 7 nm cut-off size is also maintained. Additionally, we show that insufficient droplet growth becomes more significant under the low-pressure operation. The counting efficiency of the vWCPC 3789 can vary up to 20 % for particles of different chemical compositions (e.g., ammonium sulfate and sucrose particles). However, such variation is independent of pressure.