The move came one day after he announced he would not seek re-election in November 2018.
"This afternoon I received a letter of resignation from Congressman Tim Murphy, effective October 21," House Speaker Paul Ryan said in a statement.
"It was Dr. Murphy's decision to move on to the next chapter of his life, and I support it."
Murphy, an eight-term congressman from Pennsylvania, has been popular with members of the pro-life movement, and recently sponsored legislation that criminalizes most abortions after the 20th week of pregnancy.
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The bill is unlikely to pass the Senate, where Democratic blocking tactics could derail it.
Criticism of Murphy surged when the Pittsburgh Post- Gazette broke a story about the lurid sex scandal just as the House of Representatives voted on Murphy's bill.
Murphy, 65, acknowledged last month that he had an extramarital affair with Shannon Edwards, a psychologist who worked with him on mental health legislation.
On Tuesday the Gazette reported that Edwards sent Murphy a text message in January that excoriated him for an anti- abortion statement on his Facebook account.
Another Republican pro-life congressman, Scott DesJarlais, faced a similar abortion scandal in 2012, but he remains in Congress.