The overnight operation targeting the station's Ramallah offices was the latest attempt to silence Palestinian broadcasters Israel believes are fueling a five-month wave of violence.
The Shin Bet charged that the channel "broadcasts on behalf of the Islamic Jihad" group and said it had closed it in a joint operation with the army, AFP reported.
Israeli forces arrested Palestine Today manager, Farooq Aliat, 34, of Bir Zeit, north of Ramallah.
Cameraman Mohammed Amr and technician Shabib Shabib were also arrested, the Palestinian Journalists Union said.
A wave of violence has killed 188 Palestinians, 28 Israelis, two Americans, an Eritrean and a Sudanese since October 1, according to an AFP count.