Khalil Adel Khalil, born in 1990 and a resident of A-Tur neighbourhood, had been inspired by IS videos and in August resolved to join it in Syria, a Shin Bet statement said.
It said Khalil, who worked as a para-medical assistant at a state-owned psychiatric hospital, used sports facilities at Jerusalem's Hebrew University to physically prepare for combat in the ranks of IS, which holds swathes of territory in Syria and Iraq.
He is alleged to have flown from Israel to Greece and then to Turkey where he contacted an IS agent who led him to a safe house near the border with Syria.
From there he was taken across the frontier along with a number of others seeking to join the group, the agency said.
It did not specify what Khalil did in Syria, merely noting that he returned "a few weeks later" and was subsequently arrested.
Signup to our newsletter and follow us on Facebook and Twitter!
Khalil was charged at Jerusalem district court with "attempted membership and attempted activity in an illegal organisation, trying to establish contact with a foreign agent and unlawful departure" from Israel, the statement read.
Earlier this month, IS released a video purporting to show a young boy executing an Arab Israeli "spy" from east Jerusalem by shooting him in the forehead with a pistol.
Several Arab Israelis have been convicted of trying to join Syrian rebels.
Security authorities say they know of about 30 cases of Arab Israelis who have gone to Syria to fight for jihadist groups against President Bashar al-Assad's regime, but that only a few have joined IS.
Israel considers east Jerusalem to be part of the Jewish state, even though most Palestinians who live there do not have Israeli citizenship, only residency.
Khalil's case "illustrates the security threat posed by Israelis joining IS after being exposed to propaganda disseminated by the group, primarily via the Internet," the Shin Bet statement read.
"Their return to Israel, with knowledge of and practical experience in terrorism and warfare, exposes the country to significant risks of severe terrorism."