After high school, Waggoner initially attended Auburn University, where he walked on to the basketball team. After two years at Auburn, he transferred to Birmingham-Southern College when they offered him a basketball scholarship. He graduated from Birmingham-Southern College in 1960 with a Bachelor of Arts degree. Later, he furthered his education by earning a Juris Doctorate from the Birmingham School of Law.

Waggoner's political career began at the young age of 29 when he won a seat in the Alabama House of Representatives in 1966. He served in the House until 1983, initially as a Democrat. In 1983, he switched to the Republican Party and ran unsuccessfully for the U.S. House of Representatives against Democrat Ben Erdreich in Alabama's 6th Congressional District in 1984, receiving 40% of the vote. From 1988 to 1990, he served as the Governor's legislative liaison.

In 1990, Waggoner successfully ran for the Alabama State Senate, representing District 16, which includes parts of Jefferson and Shelby Counties. He has been reelected multiple times and continues to serve in this position, making him the longest-serving legislator in Alabama history. During his tenure in the Senate, Waggoner served as Senate Minority Leader from 2002 to 2010, and after Republicans gained a legislative majority in November 2010 for the first time since Reconstruction, he became Senate Majority Leader, serving in that capacity from 2010 to 2014.

Throughout his career in the Senate, Waggoner has held numerous committee assignments. He currently chairs the Senate Rules Committee and the Local Legislation Jefferson County Committee, while serving as Vice Chair of the Confirmations Committee. He also serves on several other committees, including Banking and Insurance, Finance and Taxation Education, Finance and Taxation General Fund, and the Local Legislation Shelby County Committee.

Outside of his legislative duties, Waggoner has been active in the business community. In 1984, he established Birmingham Business Consultants, LLC, where he serves as Owner and CEO. He also previously worked as Vice President of Community and Public Affairs for HealthSouth Corporation.

Waggoner has been recognized for his contributions to Alabama. In 2021, the University of Alabama at Birmingham honored him with the President's Medal, one of its highest awards, for his leadership in the Alabama Senate and his effectiveness in collaborating with higher education, industry, and other constituencies statewide. He was also inducted into the Birmingham Southern College Sports Hall of Fame in 2007 and received the Birmingham Southern Distinguished Alumni award in 2013.

In his personal life, Waggoner is married to Marilyn Mitchell Waggoner, who was born on July 28, 1938, in Birmingham, Alabama. She is the only child of Arthur M. (Pete) Mitchell and Corry Stamps Mitchell and attended Ensley High School, Auburn University (where she pledged Phi Mu social sorority), the University of Alabama in Birmingham, and Southern Institute, studying Interior Design. Together, they have four children- Mark Waggoner, Scott Waggoner (deceased), Lyn Waggoner Kilpatrick, and Jay Waggoner. They are also the proud grandparents of seven grandchildren and have one great-grandchild. The Waggoners reside in Vestavia Hills, Alabama.

Waggoner is a member of the Homewood Church of Christ and has been active in numerous community organizations. His commitment to public service and his extensive experience in Alabama politics have made him a significant figure in the state's legislative history, with a career spanning over five decades.