Stellar high-energy radiation ( X-ray and extreme ultraviolet , XUV ) drives atmospheric escape in close-in exoplanets . Given that stellar irradiation depends on the stellar magnetism and that stars have magnetic cycles , we investigate how cycles affect the evolution of exoplanetary atmospheric escape . Firstly , we consider a hypothetical HD209458b-like planet orbiting the Sun . For that , we implement the observed solar XUV radiation available over one and a half solar cycles in a 1D hydrodynamic escape model of HD209458b . We find that atmospheric escape rates show a cyclic variation ( from 7.6 to 18.5 \times 10 ^ { 10 } g s ^ { -1 } ) , almost proportional to the incident stellar radiation . To compare this with observations , we compute spectroscopic transits in two hydrogen lines . We find non-detectable cyclic variations in Ly \alpha transits . Given the temperature sensitiveness of the H \alpha line , its equivalent width has an amplitude of 1.9 mŠvariation over the cycle , which could be detectable in exoplanets such as HD209458b . We demonstrate that the XUV flux is linearly proportional to the magnetic flux during the solar cycle . Secondly , we apply this relation to derive the cyclic evolution of the XUV flux of HD189733 using the star’s available magnetic flux observations from Zeeman Doppler Imaging over nearly a decade . The XUV fluxes are then used to model escape in HD189733b , which shows escape rate varying from 2.8 to 6.5 \times 10 ^ { 10 } g s ^ { -1 } . Like in the HD209458b case , this introduces variations in Ly \alpha and H \alpha transits , with H \alpha variations more likely to be observable . Finally , we show that a strong stellar flare would enhance significantly Ly \alpha and H \alpha transit depths .