Sam Baker held a variety of teaching, principal, and superintendent positions around the state in the years following his college graduation. Among the notable were principal at Jefferson City, Missouri in 1899 and Joplin, Missouri. After a three-year term as superintendent for Richmond, Missouri schools, Baker returned to Jefferson City as superintendent in 1913. While there he was instrumental in the issuing of a $100,000 dollar bond passage that brought large improvements to the school district. Voters statewide took notice of his efforts as a reformer and elected Baker as Missouri's Superintendent of Public Schools in 1918. Baker served as the superintendent from 1919 to 1923. During his tenure Baker was successful in securing more funding for rural schools from the state legislature, increasing teacher training and salaries, and promoting more emphasis on vocational education. Despite these improvements Baker was defeated when running for reelection in 1922 as he was edged out by Democrat Charles A. Lee by just a few hundred votes.
Governor
After his defeat in the 1922 election Sam Baker chose to continue in politics rather than in the education field. Republican incumbent governor Arthur Hyde, limited to one term by Missouri law at the time, endorsed Baker's candidacy to succeed him as governor in 1924. Baker defeated two other Republicans, including Missouri lieutenant governorHiram Lloyd, in the August primary. In the November general election Baker defeated Democrat Arthur W. Nelson by less than six thousand votes to become Missouri's 36th governor. As governor Baker continued to advocate changes and improvements for Missouri schools, including increased funding and redistricting to consolidate low-quality schools. However, the Missouri legislature, including many members of his own party, foiled Baker's efforts. Several leading Republicans were upset that Baker made political appointments based more on qualifications and friendship regardless of party instead of ones hand-picked by party leadership. Baker did have some areas of success however, including establishment of a Workers' compensation program, passage of a $75 million bond issue to improve the quality of Missouri roads, instituting banking reforms, and the development of Missouri state parks. One of the earliest parks, Sam A. Baker State Park in Wayne county, was named in the governors honor after his death.
Death
Governor Baker suffered failing health during his final year in office, and shortly after leaving office in January 1929 he suffered two major strokes. Bedridden for his remaining years, Samuel A. Baker died from a cerebral hemorrhage on September 16, 1933. He is buried in Riverview Cemetery in Jefferson City, Missouri.