Over the past 20 years, the Chandra X-ray Observatory has examined hundreds of active galactic nuclei (AGN), revealing bright and hard X-ray emission spectra from the kpc-scale jets of these sources. We present here a comprehensive archival analysis of these observations in search of evidence of short-timescale X-ray flux variability. We compared the counts and exposures associated with discrete jet knots or hotspots for different observations using a Poisson rate-ratio test. Based on current results, around 40% of all analyzed sources have at least one confirmed instance of flux variability (p < .05) of magnitude between ±30% and timescales ranging from decades to months. Variability on these scales constitutes a rejection of the dominant IC/CMB explanation of the so-called ‘anomalous’ X-ray flux and suggests the need for an alternative model such as a second synchrotron component to account for the second high-energy spectral component. More generally, it also suggests the existence of parsec-scale features much smaller than the observed kpc-scale knots and a need to reexamine jet structure and acceleration mechanisms.