Magnetars are an extreme, highly magnetized class of isolated neutron stars whose large X-ray luminosity is believed to be driven by their high magnetic field. In this work we study for the first time the possible very high energy gamma-ray emission above 100 GeV from magnetars, observing the sources 4U 0142+61 and 1E 2259+586. We observed the two sources with atmospheric Cherenkov telescopes in the very high energy range (E > 100 GeV). 4U 0142+61 was observed with the MAGIC I telescope in 2008 for ~25 h and 1E 2259+586 was observed with the MAGIC stereoscopic system in 2010 for ~14 h. The data were analyzed with the standard MAGIC analysis software. Neither magnetar was detected. Upper limits to the differential and integral flux above 200 GeV were computed using the Rolke algorithm. We obtain integral upper limits to the flux of 1.52*10^-12cm^-2 s^-1 and 2.7*10^-12cm^-2 s^-1 with a confidence level of 95% for 4U 0142+61 and 1E 2259+586, respectively. The resulting differential upper limits are presented together with X-ray data and upper limits in the GeV energy range.