The objective of this letter is to present the first experimental evidence of perturbations of GPS signals by the electron density irregularities caused by the HF‐heating of the F2 region of the ionosphere. The experiments were conducted using the HAARP heater having the radiating frequency f which matches 3 fB, i.e., triple the local electron gyro frequency. Such frequency is expected to generate super small irregularities of the electron density which can scatter GPS signals. It was found that the differential phase of the probe GPS signals changed abruptly in about 10 s after the start of the HF‐heating, and then oscillated with the heating period 20 s. The oscillations lasted for 4–5 minutes and then disappeared, presumably when the resonance condition f = 3 fB was not satisfied, although the HF‐heating continued. The phase oscillations indicate the presence of small scale irregularities of the electron density caused by the HF‐heating at the frequency matching 3 fB.