The traditional way is to pre-filter the returns thanks to the a relation similar to : $r^{f}_{t} = r_{t} /\phi_{t}$ where $r_{t}$ are the squared log returns, $r^{f}_{t}$ the filtered squared returns and $\phi_{t}$ the periodicity component. $\phi_{t}$ is a deterministic intraday component (the seasonal effect at time $t$). We estimate the GARCH model on the filtered (i.e de-seasonalized) series $r^{f}_{t}$.
There exists several models to characterise $\phi_{t}$, the one proposed by Boudt, K., Croux, C., & Laurent, S. (2011) is robust to Jumps.
The HighFrequency R package provides several routines to model the deterministic component, see here.
See also:
Andersen, T. G., & Bollerslev, T. (1997). Intraday periodicity and volatility persistence in financial markets. Journal of Empirical Finance, 4(2–3), 115–158. https://doi.org/10.1016/S0927-5398(97)00004-2
Boudt, K., Croux, C., & Laurent, S. (2011). Robust Estimation of Intraweek Periodicity in Volatility and Jump Detection. Journal of Empirical Finance, 18, 353–367. https://doi.org/10.2139/ssrn.1297371