  Motivated by the recent JWST discovery of galaxy overdensities during the
Epoch of Reionzation, we examine the physical properties of high-$z$
protoclusters and their evolution using the FLAMINGO simulation suite. We
investigate the impact of the apertures used to define protoclusters, because
the heterogeneous apertures used in the literature have limited our
understanding of the population. Our results are insensitive to the
uncertainties of the subgrid models at a given resolution, whereas further
investigation into the dependence on numerical resolution is needed. When
considering galaxies more massive than $M_\ast\,{\simeq}\,10^8\,{\rm M_\odot}$,
the FLAMINGO simulations predict a dominant contribution from progenitors
similar to those of the Coma cluster to the cosmic star-formation rate density
during the reionization epoch. Our results indicate the onset of suppression of
star formation in the protocluster environments as early as $z\,{\simeq}\,5$.
The galaxy number density profiles are similar to NFW at $z\,{\lesssim}\,1$
while showing a steeper slope at earlier times before the formation of the
core. Different from most previous simulations, the predicted star-formation
history for individual protoclusters is in good agreement with observations. We
demonstrate that, depending on the aperture, the integrated physical properties
including the total (dark matter and baryonic) mass can be biased by a factor
of 2 to 5 at $z\,{=}\,5.5$--$7$, and by an order of magnitude at
$z\,{\lesssim}\,4$. This correction suffices to remove the
${\simeq}\,3\,\sigma$ tensions with the number density of structures found in
recent JWST observations.
