Gertner was born in New York City and grew up in Flushing, New York, where she was a cheerleader, a member of the staff of her high school's literary magazine, runner-up for homecoming queen, and valedictorian of her class. Gertner received her Bachelor of Arts degree from Barnard College in 1967 and a Master of Arts and a Juris Doctor from Yale University and Yale Law School, respectively, in 1971. While attending Yale, Gertner became friends with Hillary Rodham and met Bill Clinton.
Gertner began her legal career in 1971 as a law clerk for Judge Luther Swygert of the United States Court of Appeals for the Seventh Circuit. Between 1972 and 1994, she practiced law in and around the Greater Boston area, during which she also taught at Boston University School of Law and was a visiting professor at Harvard Law School. During this period, Gertner was notable for being a supporter of liberalism and feminist ideals, wearing bright red clothes in court, carrying her legal briefs in shopping bags and keeping files on lawyers and judges she felt to be sexist.
On October 27, 1993, on the recommendations of Senators Ted Kennedy and John Kerry, Gertner was nominated to the United States District Court for the District of Massachusetts by President Bill Clinton to a seat vacated by A. David Mazzone. Gertner was confirmed by the Senate on February 10, 1994, and received her commission on February 14, 1994.
After announcing her retirement from the bench effective September 1, 2011, Gertner was appointed a Professor of Practice at Harvard Law School.
Gertner ruled in U.S. v. Hines, 55 F.Supp. 2d 62 (D.Mass. 1999), a case regarding the admissibility of expert testimony, that (i) a handwriting expert could testify to similarities between handwriting samples but not state an opinion about whether the same person wrote both notes, and (ii) expert witness testimony regarding the reliability of eyewitness testimony, including problems of cross-racial identification, was admissible. The case interpreted new admissibility standards for expert testimony set forth by the Supreme Court in Daubert v. Merrell Dow Pharmaceuticals, 509 U.S. 579 (1993) and Kumho Tire Co. v. Carmichael, 526 U.S. 137 (1999).
On July 26, 2007, she ordered the federal government to pay a record $101.7 million for withholding evidence that could have exculpated four men wrongfully convicted of murder. The men had been falsely accused by mob hitman Joseph "The Animal" Barboza, with the help of corrupt FBI agent H. Paul Rico. The government appealed the award, which was upheld in 2009 by the U.S. Court of Appeals for the First Circuit.
Judge Gertner presided over Sony BMG v. Tenenbaum, a civil trial in which the Recording Industry Association of America accused Joel Tenenbaum, a Massachusetts college student, of illegally downloading and sharing files, thus violating U.S. copyright law. In July 2009, a jury awarded $675,000 to the music companies, but Judge Gertner later reduced the award to $67,500, stating that arbitrarily high statutory damages violate due process and are thus unconstitutional. After both parties appealed, the First Circuit Court of Appeals reinstated the original damage award of $675,000 and remanded the case to the District Court, ruling that the judge should have avoided the constitutional issue by first considering remittitur. The Supreme Court refused to hear Tenenbaum's appeal arguing against the remand. A new District Court judge then found no cause for remittitur, and held that the statutory damage award was constitutional. Tenenbaum again appealed to the First Circuit, which in June 2013 upheld the award.
As a defense attorney, she defended Brandeis University student and fugitive Susan Saxe, who stole money to finance the student strikes during the Vietnam era. Gertner describes the Saxe trial as her first big case.
Gertner is to date the only Massachusetts judge to post to a personal blog. Though this has resulted in some criticism, Gertner maintains that judges are often too silent on issues they should publicly address.
Gertner published her memoirs, In Defense of Women: Memoirs of an Unrepentant Advocate, in 2011. The book focuses on the period during which she worked as a criminal defense and civil rights lawyer before joining the Federal bench in 1994.
Gertner is married to John Reinstein, former Legal Director for the Massachusetts ACLU.
In October 2015, Gertner became the subject of media attention in the Boston area when an escaped cockatoo did considerable damage to her Brookline residence, a historic Victorian home which also happened to be the birthplace of Robert F. Kennedy. After eluding capture for several months, the bird was caught on October 22.2008 Thurgood Marshall Award of the American Bar Association, recognizing Gertner's contributions to advancing human rights and civil liberties.
2014 Margaret Brent Women Lawyers of Achievement Award of the American Bar Association, recognizing Gertner's advocacy, mentoring and achievements in the legal field.