Malone said in a statement that he resigned from the board in order to cut down on his travel and focus himself on fewer board positions.
"I remain heavily invested in Charter, both financially and emotionally, and am excited about its prospects," Malone said in a statement.
The longtime media executive was appointed to Charter's board in 2013 as Liberty Broadband's nominee. In his stead, Liberty nominated Sirius XM CEO James Meyer.
Malone is a widely respected figure in the media and cable industries. A savvy dealmaker, Malone built his cable empire TCI in the 1970s before selling it to AT&T in 1999 for roughly $50 billion.
The Liberty Media chairman also serves as a director on the board of Discovery Communications, which closed its $15 billion acquisition of Scripps Networks in March. He was also chairman and CEO of Discovery when it became a public company.