After graduating from New York City public schools, Thompson attended John Jay College of Criminal Justice, where he graduated magna cum laude.
He then attended the New York University School of Law, where he earned the Arthur T. Vanderbilt Medal for his outstanding contributions to the law school community.
Thompson began as an attorney in the United States Treasury Department in Washington, D.C., where he served as Special Assistant to former Treasury Department Undersecretary for Enforcement and now the Secretary General of Interpol, Ronald K. Noble.
Thompson then became a federal prosecutor, who served in the United States Attorney's Office in Brooklyn. As an Assistant U.S. Attorney, Thompson was a member of the federal prosecution team. His team got former New York City Police Department Officer Justin Volpe, who sodomized Abner Louima inside a bathroom at the 70th Precinct in Brooklyn, to plead guilty during the middle of his trial.
After his time as a federal prosecutor, Thompson went into private practice, first at an international law firm and then at his own law firm, Thompson Wigdor LLP, which he co-founded in 2003. Thompson worked with Senator Charles E. Schumer, Congresswoman Yvette D. Clarke, other elected officials, and members of the clergy to convince the United States Department of Justice to reopen the investigation into the 1955 murder of 14-year-old Emmett Till in Mississippi.
In 2011, he represented Nafissatou Diallo, the hotel housekeeper who claimed that she was sexually assaulted in a Manhattan hotel room by Dominique Strauss-Kahn, the former head of the International Monetary Fund. Her case was dropped by prosecutors, who stated that they were not convinced of his culpability beyond a reasonable doubt due to serious issues in Diallo's credibility and inconclusive physical evidence, and therefore could not ask a jury to believe it.
In September 2013, Ken Thompson defeated incumbent Charles J. Hynes in the Democratic primary, where he ran as a critic of the NYPD.
Thompson is the first challenger to defeat a sitting District Attorney in Brooklyn since 1911, and the first African-American district attorney of Kings County.
Thompson took office on January 1, 2014. District Attorney Thompson died on October 9, 2016 at Memorial Sloan Kettering Hospital after a hard fought battle with cancer, with his family at his side.