The call came after months of clashes in and around annexed east Jerusalem and a growing number of deadly Palestinian attacks by lone individuals.
So far, the Palestinian leadership has not taken a clear position on the violence, which has recently spread to Arab areas of Israel as well as the West Bank.
In a letter to mark 10 years since the death of veteran leader Yasser Arafat, Barghuti said that "choosing global and armed resistance" was being "faithful to Arafat's legacy, to his ideas and his principles for which tens of thousands died as martyrs."
Barghuti, who is widely believed to have masterminded the second Palestinian intifada, from 2000 to 2005, wrote the letter from his cell in Israel's Hadarim prison where he is serving five life sentences for attacks on Israeli targets.
A senior figure within the Fatah movement of Palestinian president Mahmud Abbas, Barghuti was arrested in 2002 and sentenced two years later.
Barghuti has since said he never supported attacks on civilians inside Israel and in recent years has thrown his support behind peaceful resistance.
"Barghuti was arrested in 2002 and sentenced two years later"
He still wields huge influence from inside prison and is considered the only serious challenger to Abbas as president, with surveys regularly naming him as favourite to win elections should he be released from jail.
Signup to our newsletter and follow us on Facebook and Twitter!
"It is imperative to reconsider our choice of resistance as a way of defeating the occupier," he wrote.
There has been increasing talk of a new intifada in the making following months of clashes in annexed east Jerusalem and the series of deadly attacks.
The unrest has recently spread into Israel and the West Bank, with two Israelis killed in two separate stabbing attacks on Monday.
With religious tensions also surging at the flashpoint Al-Aqsa mosque compound in Jerusalem, a site holy to both Muslims and Jews, Barghuti urged the Palestinian leadership to take action and make good on threats to end security cooperation with Israel.
"The Palestinian Authority must review its priorities and its mission... and put an immediate end to security cooperation which is only strengthening the occupier," he said.
He also remarked on the circumstances of Arafat's death, saying his "assassination" was the result of "an official Israeli-American decision".
Arafat died in a military hospital near Paris on November 11, 2004 in circumstances that have never been clear.
Two years ago, Swiss experts who examined his personal effects reported finding "abnormal" levels of polonium, an extremely radioactive toxin, fuelling the widespread Palestinian belief that he was poisoned by Israel.
Israel has repeatedly denied any role in Arafat's death.