We report on slow phase variations of the response of the space-ground radio interferometer RadioAstron during observations of pulsar B0329+54. The phase variations are due to the ionosphere and clearly distinguishable from effects of interstellar scintillation. Observations were made in a frequency range of 316-332~MHz with the 110-m Green Bank Telescope and the 10-m RadioAstron telescope in 1-hour sessions on 2012 November 26, 27, 28, and 29 with progressively increasing baseline projections of about 60, 90, 180, and 240 thousand kilometres. Quasi-periodic phase variations of interferometric scintles were detected in two observing sessions with characteristic time-scales of 12 and 10 minutes and amplitudes of up to 6.9~radians. We attribute the variations to the influence of medium-scale Travelling Ionospheric Disturbances. The measured amplitude corresponds to variations in vertical total electron content in ionosphere of about $0.1times10^{16}, mathrm{m}^{-2}$. Such variations would noticeably constrain the coherent integration time in VLBI studies of compact radio sources at low frequencies.
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