Context. High-mass gamma-ray binaries are powerful nonthermal galactic sources, some of them hosting a pulsar whose relativistic wind interacts with a likely inhomogeneous stellar wind. So far, modeling these sources including stellar wind inhomogeneities has been done using either simple analytical approaches or heavy numerical simulations, none of which allow for an exploration of the parameter space that is both reasonably realistic and general. Aims. Applying different semi-analytical tools together, we study the dynamics and high-energy radiation of a pulsar wind colliding with a stellar wind with different degrees of inhomogeneity to assess the related observable effects. Methods. We computed the arrival of clumps to the pulsar wind-stellar wind interaction structure using a Monte Carlo method and a phenomenological clumpy-wind model. The dynamics of the clumps that reach deep into the pulsar wind zone was computed using a semi-analytical approach. This approach allows for the characterization of the evolution of the shocked pulsar wind region in times much shorter than the orbital period. With this three-dimensional information about the emitter, we applied analytical adiabatic and radiative models to compute the variable high-energy emission produced on binary scales.Results. An inhomogeneous stellar wind induces stochastic hour-timescale variations in the geometry of the two-wind interaction structure on binary scales. Depending on the degree of stellar wind inhomogeneity, 10-100% level hour-scale variability in the X-rays and gamma rays is predicted, with the largest variations occurring roughly once per orbit. Conclusions. Our results, based on a comprehensive approach, show that present X-ray and future very-high-energy instrumentation can allow us to trace the impact of a clumpy stellar wind on the shocked pulsar wind emission in a gamma-ray binary.