A number of studies have revealed variability from neutron star low-mass X-ray binaries during quiescence. Such variability is not well characterised, or understood, but may be a common property that has been missed due to lack of multiple observations. One such source where variability has been observed is Aql X-1. Here, we analyse 14 Chandra and XMM-Newton observations of Aql X-1 in quiescence, covering a period of approximately 2 years. There is clear variability between the epochs, with the most striking feature being a flare-like increase in the flux by a factor of 5. Spectral fitting is inconclusive as to whether the power-law and/or thermal component is variable. We suggest that the variability and flare-like behaviour during quiescence is due to accretion at low rates which might reach the neutron star surface.