Thomas was born and raised on Chicago's South Side. Thomas's father was a postal clerk and his mother a former secretary. Thomas's uncle, a Chicago police officer, also lived with the family. Thomas graduated from Mount Carmel High School, where he had an outstanding record in national debate competitions. He and his twin brother, John, reached the semi-finals of the Georgetown Summer Tournament, the first time a team from Chicago had advanced that far in the tournament.

Thomas enrolled in Boston College and continued his activities in intercollegiate debate and was invited to participate in the Fulton Prize debate during his senior year. Thomas helped pay for his studies with student loans and part time work, including work as a dishwasher in a dorm cafeteria. After graduating in 1974, Thomas found work in Chicago as a law clerk in a small law office, where he learned the court system from the bottom up and served as a process server for eviction cases on Chicago's west side. He then worked as a law librarian at Chicago-Kent College of Law. Thomas applied to graduate school at the University of Chicago and was accepted in 1975.
Thomas worked full time, first at United Parcel Service, then as a benefit authorizer at the Social Security Administration while earning a master's degree in international relations from the University of Chicago in 1979. Thomas studied with Arthur Laffer, Sol Tax and Jeremy Azrael. Thomas used his annual leave vacation time to commute from the loop to Hyde Park to take classes, while working more overtime than any of the 2,300 employees at the SSA office. Thomas applied to law school and was accepted by DePaul University College of Law in 1980.

Thomas really wanted to be a lawyer so he found work as a court clerk at Baker & McKenzie, a job that paid $3.75-$7.00 per hour He worked full time while completing law school in 27 months, with an internship at the US Department of Justice during his final summer at DePaul. Thomas landed a clerkship with the honorable William G. Clark at the Illinois Supreme Court between 1983 and 1984.

Between 1985 and 1993, Thomas worked at private law firms in Chicago and Tokyo. Thomas has logged more than 2000 court appearances in courts ranging from traffic court to the U.S.  court of appeals. Thomas has handled a wide range of litigation matters including divorce, bankruptcy, DUI, class actions, trademark, copyright, zoning, probate, personal injury, election law and immigration.
Thomas has extensive trial experience and has tried many cases to verdict. these trials include cases involving employment discrimination, arson, tenant eviction, breach of a mainframe computer lease, child custody and insurance coverage.

From 1981 to the present, Thomas undertook the study of Japanese in his spare time, studying at Harold Washington College, International Christian University and Sony Language Lab in Tokyo, as well as the Midwest Buddhist Temple and Chicago Buddhist Temple in Chicago. Thomas became one of a handful of American attorneys who speak Japanese fluently. Thomas also took a class as a returning scholar at the University of Chicago Graduate School of Business that was taught in the Japanese language.

In 1993, Thomas decided to use his Japanese language skills to help American companies, so he hung out a shingle and started the Law Offices of Thomas Flannigan. Thomas has continued to work 6 a or 7 days a week on a wide variety of legal matters in all courts great and small. In the past year, he has devoted a large part of his time to a major trademark infringement case, winning a bet your company case for a small Colorado firm that had been sued by a big electrical products company in U.S. District Court in Connecticut.

Thomas married Ellen Flannigan in August 1988. Ellen is a judge in the Circuit Court of Cook County, elected in 2006. Thomas was her campaign manager and biggest supporter.

Thomas is one of the most widely traveled attorneys in the world, having visited over 180 countries during 15 journeys around the world between 1978 and 2016.

Thomas and his wife Ellen co-authored the first book written about Tokyo's Museums: Tokyo Museums, A Complete Guide (Tuttle 1993). Thomas has also written many articles on legal and international matters and has appeared on local television programs including WTTW's Chicago Tonight. In 1987, Thomas and Ellen founded the Chicago chapter of the Traveler's Century Club, an organization for individuals who have visited more than 100 countries. Thomas and Ellen have two daughters: Erin, born in May 2002, and Megan, born in August, 2003. Thomas's twin brother is also an attorney and was a professor of English at Prairie State College. His sister is a legal secretary and his nephew survived two tours of duty with the U.S Army in Iraq.