The army arrested overnight the "senior operative" in Arraba near Jenin in the north of the occupied West Bank, Israel's military said.
A source with Islamic Jihad confirmed that one of its leaders, Tareq Qadaan, was detained as part of an "arrest campaign".
There were no immediate details on whether others were arrested.
Tensions have risen between Israel and Islamic Jihad after the army blew up a tunnel that stretched from the Gaza Strip into Israeli territory on October 30.
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The operation resulted in the deaths of at least 12 Palestinian militants from Hamas and Islamic Jihad.
Israeli Prime Minister Benjamin Netanyahu yesterday warned Palestinian militants in Gaza against carrying out attacks in revenge for the operation.
Islamic Jihad meanwhile threatened to hit back at Israel over the destruction of the tunnel it says it dug.
The heated rhetoric comes at a sensitive time for the Palestinians, who are seeking to follow through on a landmark reconciliation deal between rivals Fatah and Hamas, the Islamist moved which runs Gaza.
Israel and militants in Gaza have fought three wars since 2008.
The UN special coordinator for the Middle East peace process, Nickolay Mladenov, expressed concern, saying "the reckless actions and statements of militants in Gaza risk a dangerous escalation".
Hamas is allied with Islamic Jihad, which maintains a strong presence in the Gaza Strip. It is also present in the West Bank.
Hamas's statements following the tunnel operation have been less forceful as it seeks to follow through on the Palestinian reconciliation accord.
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