The Shin Bet security service said the 17-year-old had been arrested last month after crossing from the Gaza Strip into Israel "on his own".
The suspect, who as a minor cannot be identified, was the second Gazan 17-year-old allegedly involved in tunnelling to be charged by Israel in a month.
In addition to those two, another man, 29-year-old Mahmud Atawnah, was also charged over his alleged part in the militant group's tunnel network in May.
"The perpetrator conveyed valuable information regarding Hamas activities in the northern Gaza Strip and especially Hamas's offensive tunnels," a statement said.
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It alleged that "it was also revealed that Hamas is operating to establish multiple tunnels deep within the Gaza Strip connected to the offensive tunnels infiltrating Israel".
The suspect was charged at Beersheba district court in southern Israel for a series of felonies including "membership in a terror group, weapons offences and infiltrating Israel", a justice ministry spokeswoman told AFP.
The violence was the worst flare-up between the army and Hamas since a devastating 2014 war, with Hamas attacking forces operating nearby with mortar rounds and Israel responding with air raids and tank fire, which resulted in the death of a Gaza woman.
Hamas has an extensive network of tunnels inside Gaza, including those extending towards Israel and Egypt.