Born in Beckum, Germany as Helmut Ostermann, Avnery and his family emigrated to Palestine in 1933, fleeing the Nazi regime. He attended school in Nahalal and then in Tel Aviv, leaving after 7th grade, at age 14, in order to help his parents. He started work as a clerk for a lawyer, a job he held for five years or so.

He joined the Irgun, a Revisionist Zionist paramilitary group, in 1938 and wrote for some of their internal publications. At one point he edited the internal Revisionist journal Ba-Ma'avak ("in the Struggle").He started writing for independent publications at the age of 17. He left the Irgun in 1942 after becoming disenchanted with their tactics, stating in a 2003 interview that, "I didn't like the methods of terror applied by the Irgun at the time", noting he did not back killing people in retaliation for similar acts by the Arabs. In 1947 Avnery started his own small group, Eretz Yisrael Hatze'ira ("Young Land of Israel"), which published the journal Ma'avak ("Struggle"). Avnery's early political thought was influenced by Canaanism; in 1947 he proposed a union of the countries in the "Semitic region": Palestine, Transjordan, Lebanon, Syria, and Iraq.

During the 1948 Arab-Israeli War Avnery fought on the southern front in the Givati Brigade as a squad commander, and later in the Samson's Foxes commando unit (and also wrote its anthem). He wrote dispatches from the front line which were published in Haaretz and later as a book, In the Fields of Philistia (, Bi-Sdot Pleshet). Avnery was wounded twice, the second time, toward the end of the war, seriously; he spent the last months of his army service convalescing and was discharged in the summer of 1949.

After briefly working at Haaretz, in 1950 Avnery (with Shalom Cohen and two others) bought the failing magazine HaOlam HaZeh ("This World"). Avnery edited the weekly magazine during the 1950s and the 1960s Avnery, turning it into an anti-establishment tabloid known for many sensational scoop and for featuring nudes on its back cover. The formula seemed to work, as for many years it was Israel's leading alternative-media publication.

After the Egyptian Revolution of 1952 Avnery used his editorials in HaOlam HaZeh to call for a preventive war against Egypt, arguing that "the reactionary Arab regimes" would attack Israel "the minute Arab superiority in weapons over Israel is great enough." He began to revise his views after the 1956 Suez Crisis, which ended in Israeli withdrawal and strengthened Nasser. In June 1957 Avnery suggested that Israel aid Palestinians in overthrowing the Hashemite monarchy in Jordan (a "product of imperialism"); Israel would then form a federation with the new Palestinian Jordanian state. In the late 1950s Avnery was among the founders of the group Semitic Action, which argued for a regional federation of Israel and its neighbors.

In 1965 Avnery created a political party bearing the name of his and Cohen's magazine, HaOlam HaZeh — Koah Hadash, and was elected to the Knesset in the 1965 election. Although he retained his seat in the 1969 election, the party disintegrated and Avnery renamed it Meri. Although it failed to win any seats in the 1973 elections, Avnery returned to the Knesset as a member of the Left Camp of Israel after the 1977 election, but did not retain his seat in the 1981 election. He was later involved in the Progressive List for Peace.

In late 1975 Avnery was among the founders of the Israeli Council for Israeli-Palestinian Peace. Shortly after the group's founding, Avnery was assaulted and stabbed several times.

Avnery famously met Yasser Arafat on 3 July 1982, during the Siege of Beirut ... said to have been the first time an Israeli met personally with Arafat.

He later turned to left-wing peace activism and founded the Gush Shalom movement in 1993, which he continues to lead as of 2009. He is a secularist and strongly opposed to the Orthodox influence in religious and political life.

In 2001, Avnery and his wife Rachel Avnery were honoured with the Right Livelihood Award, sometimes called the "Alternative Nobel Prize", " for their unwavering conviction, in the midst of violence, that peace can only be achieved through justice and reconciliation". In 2006, settler activist Baruch Marzel called on the Israeli military to carry out "a targeted killing" against Avnery. In 2010, he was assaulted by thugs in the aftermath of the Gaza flotilla raid.

Avnery is a contributor to the news and opinion sites CounterPunch, Information Clearing House, Scoop.co.nz LewRockwell.com and The Exception Magazine.

"You can’t talk to me about terrorism, I was a terrorist." (referring to his Irgun activities).

"I myself am a 100% atheist. And I am increasingly worried that the Israeli-Palestinian struggle, which dominates our entire life, is assuming a more and more religious character."

"I define myself as a post-Zionist - I recognize Zionism and its importance but believe that that chapter in our history is over and we need to move forward."

"The Government of Israel has insulted the Vice President of the United States, and spat in the face of the President ... they wiped the spit off their faces and smiled politely ... as the saying goes: when you spit in the face of a weakling, he pretends that it is raining" Uri Avnery 13/3/2010.