Her father, Georgy Alikhanov (Armenian name Gevork Alikhanyan), was an Armenian who founded the Soviet Armenian Communist Party, and was a highly placed member of the Comintern; her mother, Ruf, (Ruth Bonner), was a Jewish Communist activist. In 1937, Bonner's father was arrested by the NKVD and executed as part of Stalin's Great Purge; her mother was arrested a few days later, and served eight years in a forced labor camp near Karaganda, Kazakhstan, followed by nine years of internal exile. Bonner's 41-year-old maternal uncle, Matvei Bonner, was also executed during the purge, and his wife internally exiled. All four were exonerated (rehabilitated) following Stalin's death in 1953. Serving as a nurse during World War II, Bonner was wounded twice, and in 1946 was honorably discharged as a disabled veteran. After the war she earned a degree in pediatrics from the First Leningrad Medical Institute, presently First Pavlov State Medical University of St. Petersburg.

Beginning as early as the 1940s, Bonner had helped political prisoners and their families. Although Bonner had joined the Soviet Communist Party in 1964 while she was working as a physician, only a few years later she was becoming active in the Soviet human rights movement. Her resolve towards dissidence was strengthened in August 1968 after Soviet bloc tanks rolled into Czechoslovakia in order to crush the Prague Spring movement. That event strengthened her belief that the system could not be reformed from within. At the Kaluga trial in 1970, Bonner and Sakharov met Natan Sharansky and began working together to defend Jews sentenced to death for attempting an escape from the USSR in a hijacked plane. Under pressure from Sakharov, the Soviet regime permitted Yelena Bonner to travel to the West in 1975, 1977 and 1979 for treatment of her wartime eye injury. When Sakharov, awarded the 1975 Nobel Peace Prize, was barred from travel by the Soviet authorities, Bonner, in Italy for treatment, represented him at the ceremony in Oslo.

Bonner became a founding member of the Moscow Helsinki Group in 1976. When in January 1980 Sakharov was exiled to Gorky, a city closed to foreigners, the harassed and publicly denounced Bonner became his lifeline, traveling between Gorky and Moscow to bring out his writings. Her arrest in April 1984 for “anti-Soviet agitation and propaganda” and sentence to five years of exile in Gorky disrupted their lives again. Sakharov’s several long and painful hunger strikes forced the new Soviet leader, Mikhail Gorbachev to let her travel to the U.S. in 1985 for sextuple bypass heart surgery. Prior to that, in 1981, Bonner and Sakharov went on a dangerous but ultimately successful hunger strike to get Soviet officials to allow their daughter-in-law, Yelizaveta Konstantinovna (“Lisa”) Alexeyeva, an exit visa to join her husband, Bonner's son Alexei Semyonov, in the United States. In December 1986, Gorbachev allowed Sakharov and Bonner to return to Moscow.

Bonner remained outspoken on democracy and human rights in Russia and worldwide. She joined the defenders of the Russian parliament during the August Coup and supported Boris Yeltsin during the constitutional crisis in early 1993. In 1994, outraged by what she called “genocide of the Chechen people”, Bonner resigned from Yeltsin's Human Rights Commission and was an outspoken opponent to Russian armed involvement in Chechnya and critical of the Kremlin for allegedly returning to KGB-style authoritarianism under Vladimir Putin. She was also critical of the international “quartet” two-state solution to the Israel-Palestinian conflict and has expressed fears about the rise of anti-semitism in Europe.

Bonner was among the 34 first signatories of the online anti-Putin manifesto “Putin must go”, published 10 March 2010. Her signature was the first.

Her books include Alone Together and Mothers and Daughters, and she was the recipient of the Truman-Reagan Medal of Freedom; Rafto Prize; the European Parliament’s Robert Schuman Medal; awards from the International Humanist and Ethical Union, World Women's Alliance, Adelaida Ristori Foundation, and U.S. National Endowment for Democracy; Lithuanian Commemorative Medal of 13 January; Czech Republic Order of Tomas Garrigue Masaryk; and Giuseppe Motta Medal.