We model synchrotron and inverse Compton flares in blazars from radio to X‐rays and gamma‐rays. We take into account the internal structure and geometry of the source (energy stratification) caused by particle acceleration at shock wave fronts and synchrotron energy losses. We also consider the effects of light‐travel time of the synchrotron emission that supplies the seed photons for synchrotron self‐Compton scattering. These internal light‐travel delays may lead to a lag of the higher energy flare with respect to variations at lower frequencies. In the model, a flare in the jet follows a collision between moving and stationary shocks. The collision leads to the creation of forward and reverse shocks, both advecting down the jet along with the shocked plasma, but moving in opposite directions in the shocked plasma rest frame. The double shock‐wave structure of the emission region could be apparent in the flare profile and can provide an explanation for large time delays between synchrotron and inverse Compton flares. © 2004 American Institute of Physics