The Kepler mission has been providing high-quality photometric data leading to many breakthroughs in the exoplanet search and in stellar physics. Stellar magnetic activity results from the interaction between rotation, convection, and magnetic field. Constraining these processes is important if we want to better understand stellar magnetic activity. Using the Sun, we want to test a magnetic activity index based on the analysis of the photometric response and then apply it to a sample of M dwarfs observed by Kepler. We estimate a global stellar magnetic activity index by measuring the standard deviation of the whole time series, S ph. Because stellar variability can be related to convection, pulsations or magnetism, we need to ensure that this index mostly takes into account magnetic effects. We define another stellar magnetic activity index as the average of the standard deviation of shorter subseries which lengths are determined by the rotation period of the star. This way we can ensure that the measured photometric variability is related to starspots crossing the visible stellar disc. This new index combined with a time-frequency analysis based on the Morlet wavelets allows us to determine the existence of magnetic activity cycles. We measure magnetic indexes for the Sun and for 34 M dwarfs observed by Kepler. As expected, we obtain that the sample of M dwarfs studied in this work is much more active than the Sun. Moreover, we find a small correlation between the rotation period and the magnetic index. Finally, by combining a time-frequency analysis with phase diagrams, we discover the presence of long-lived features suggesting the existence of active longitudes on the surface of these stars.