Thiele began his political career as counsel to former Assemblyman John L. Behan, a position in which he served until 1982. Subsequent to his service as a legislative assistant he became Southampton Town Attorney and East Hampton Town Planning Board Attorney, from 1982 to 1987 and 1982 to 1986 respectively. In 1987, Thiele won a bid to represent the 16th District within the Suffolk County Legislature, a position he would hold for the subsequent four years. After serving in the Suffolk County Legislature he would go on to be elected as Southampton town supervisor, where he would serve until winning a 1995 special election to succeed his former boss in the State Assembly. Although elected as a Republican, after being elected to the Suffolk County Legislature, he joined the chamber's nine Democrats to elect a Democrat as presiding officer.
In 1995, Republican Governor George Pataki appointed Assemblyman John L. Behan as New York State Commissioner of Veterans' Affairs. Behan resigned from the New York Assembly, leaving a vacant seat in the 2nd District. Thiele ran for the seat and defeated Democratic nominee Leo Davis 69%–28% in the March 1995 special election. He won re-election to his first full term with 62% of the vote. Between 1998 and 2006, he never won re-election with less than 59% of the vote. In 2008, he defeated Democratic nominee Michael Pitcher 62%–38%. He won re-election for the first time as a member of the Independence Party, defeating Republican nominee Richard A. Blumenthal 59%–41%. After the installation of a new radioactive material monitoring system in Brookhaven in 2000 Thiele, along with Alec Baldwin and county legislator George Guldi, explained how the system worked. Thield announced on October 1, 2009 that he was joining the Independence Party, saying the Republicans no longer stood for "pocketbook issues" and was given permission to caucus with the Democratic super majority along with the other Independence Party assemblyman, Timothy P. Gordon Thiele, the only Independent in the Assembly, supports an open primary in New York State and supported Bernie Sanders in the 2016 Democratic Primary. Before his switch, Thiele had been ranking minority member on the Assembly Education Committee and vice chairman of the Assembly Minority Joint Conference Committee. He currently sits on the House Committee on Education, House Committee on Election Law, House Committee on Environmental Conservation, House Committee on Oversight, House Committee on Transportation, and House Committee on Ways and Means.