In 1988, Baker helped start the Pioneer Institute for Public Policy Research, an independent, nonpartisan state think tank. Baker left Pioneer in January, 1991 to join the newly elected Weld/Cellucci Administration as Undersecretary for Health in the Executive Office of Health and Human Services. As Undersecretary, Charlie played pivotal roles in Medicaid reform, facility consolidation, and the expansion of a number of key public health programs. He became Secretary of Health and Human Services in the fall of 1992, and led the Administration’s efforts to enact welfare reform.

Baker became Secretary of Administration and Finance in the fall of 1994, and served in that position until September of 1998. He re-structured and simplified the state’s purchasing system, led a major effort to improve the state’s capacity to collect third party revenue, and oversaw the largest effort ever to modernize the state’s code of regulation. He received the Distinguished Service Award from the National Governor’s Association in 1998.

Baker became CEO of Harvard Vanguard Medical Associates (HVMA) in the fall of 1998, and was soon recruited by Harvard Vanguard’s parent – Harvard Pilgrim Health Care – to serve as its CEO in May, 1999. Baker led a major turnaround at HPHC, which included a $220 million year-to-year improvement in financial performance from 1999 to 2000, and the amicable separation of HPHC and HVMA. Under Baker's tenure, HPHC went on to become the highest ranked health plan in the country for member satisfaction and clinical effectiveness for five years running, and was named a Boston Business Journal “Best Places To Work” for seven straight years.

Over the years, Baker and his wife, Lauren, have been heavily involved in numerous civic and charitable endeavors. Charlie served for 3 years as a member of the Board of Selectmen in Swampscott, and served on the town’s School Building Committee. Lauren was the registrar for Swampscott soccer for ten years, is active with the Red Cross, and serves as the Chair of the Board of Marian Court College. Charlie and his wife live in Swampscott, and have three children – Charlie, AJ, and Caroline.