Ms. Wilson is a longtime antitrust lawyer, and was nominated to the F.T.C. by President Donald J. Trump in 2018. The F.T.C. has five commissioners.

“My fundamental concern with her leadership of the commission pertains to her willful disregard of congressionally imposed limits on agency jurisdiction, her defiance of legal precedent and her abuse of power to achieve desired outcomes,” Ms. Wilson wrote of Ms. Khan.

Ms. Khan said in a joint statement with two Democratic F.T.C. commissioners, Rebecca Slaughter and Alvaro Bedoya, “While we often disagreed with Commissioner Wilson, we respect her devotion to her beliefs and are grateful for her public service.”

Ms. Wilson’s departure is expected to put greater political pressure on the agency, which Republican lawmakers and businesses have criticized for being too tough on companies. Congress controls the budgets of agencies and can threaten to curtail the F.T.C.’s powers via its power over funding. It can also call Ms. Khan to appear in public oversight hearings.

Ms. Khan has defended her actions, saying the agency’s permissive approach to mergers over decades had allowed companies like Google, Meta and Amazon to balloon in size and eat up competition. She has pushed the agency to take on riskier cases that it may not even win.