Abba Kovner was born in the Crimean Black Sea port city of Sevastopol but soon moved with his family to Vilnius (then in Poland, now in Lithuania) where he grew up and was educated at the secondary Hebrew academy and the school of the arts. While pursuing his studies, he joined and became an active member in the socialist Zionist youth movement HaShomer HaTzair.

In June 1941, Nazi Germany attacked the city, which was by that time in Lithuanian SSR, and after occupation established the Vilna Ghetto. Kovner managed to escape with several friends to a Dominican convent headed by Anna Borkowska in the city's suburbs, but he soon returned to the ghetto. He concluded that in order for any revolt to be successful, a Jewish resistance fighting force needed to be assembled. He commanded the United Partisan Organization in the forests near Vilnius and engaged in sabotage and guerrilla attacks against the Nazis. He continued his partisan efforts throughout the war and survived the Holocaust.

After liberation of Vilnius by the Soviet Red Army in July 1944, he became one of the founders of the Berihah movement, helping Jews escape Eastern Europe after the war. He came to Palestine for a short period of time in 1945, and then returned to Europe to, with the Nakam organization, continue underground activities against Nazi POW's.

Abba Kovner founded Nakam (Dam Yehudi Nakam - "Jewish Blood Will Be Avenged") as a Jewish organization with the aim of avenging the Holocaust. Nakam attempted a mass assassination on April 14, 1946 at the Langwasser internment camp near Nuremberg. Bread for 12,000 to 15,000 German POWs (mostly SS members) was reputedly painted with diluted arsenic. According to the New York Times in 1946, 207 of the interned soldiers fell ill and were admitted into the hospital but none died. Kovner was detained and deported from Europe back to Israel, where he eventually served as an officer in the Givati Brigade in the Israel War of Independence. During his service he authored "battle leaflets," designed to keep up morale.

His book of poetry Ad Lo-Or, ("Until No-Light"), 1947, describes in lyric-dramatic narrative the struggle of the Resistance partisans in the swamps and forests of Eastern Europe. Ha-Mafteach Tzalal, ("The Key Drowned"), 1951, is also about this struggle. Pridah Me-ha-darom ("Departure from the South"), 1949, and Panim el Panim ("Face to Face"), 1953, continue the story with the Israeli War of Independence.