We present the first comprehensive study of short-timescale chromospheric Hα variability in M dwarfs using the individual 15 minute spectroscopic exposures for 52, 392 objects from the Sloan Digital Sky Survey. Our sample contains about 103-104 objects per spectral type bin in the range M0-M9, with a typical number of three exposures per object (ranging up to a maximum of 30 exposures). Using this extensive data set, we find that about 16% of the sources exhibit Hα emission in at least one exposure, and of those about 45% exhibit Hα emission in all of the available exposures. As in previous studies of Hα activity (L Hα/L bol), we find a rapid increase in the fraction of active objects from M0-M6. However, we find a subsequent decline in later spectral types that we attribute to our use of the individual spectra. Similarly, we find saturated activity at a level of L Hα/L bol ≈ 10–3.6 for spectral types M0-M5 followed by a decline to about 10–4.3 in the range M7-M9. Within the sample of objects with Hα emission, only 26% are consistent with non-variable emission, independent of spectral type. The Hα variability, quantified in terms of the ratio of maximum to minimum Hα equivalent width (R EW), exhibits a rapid rise from M0 to M5, followed by a plateau and a possible decline in M9 objects. In particular, variability with R EW gsim 10 is only observed in objects later than M5, and survival analysis indicates a probability of lesssim0.1% that the R EW values for M0-M4 and M5-M9 are drawn from the same distribution. We further find that for an exponential distribution, the R EW values follow N(R EW) ∝ exp[ – (R EW – 1)/2.3] for M0-M4 and ∝exp[ – (R EW – 1)/2.9] for M5-M9. Finally, comparing objects with persistent and intermittent Hα emission, we find that the latter exhibit greater variability. Based on these results, we conclude that Hα variability in M dwarfs on timescales of 15 minutes to 1 hr increases with later spectral type, and that the variability is larger for intermittent sources.