The centre-forward was sent off in the second half of his side's 2-0 home win over Swansea City on Saturday when he caught Chico Flores with a trailing arm.
The contact appeared to be both minimal and accidental, prompting the Hammers to contest the charge, but the FA have dismissed the claim meaning Carroll will serve his three-game sanction.
"West Ham United's Andy Carroll will serve a three-match suspension with immediate effect after his claim of wrongful dismissal was rejected by an Independent Regulatory Commission," read an FA statement.
"Carroll was dismissed for violent conduct during West Ham's game against Swansea City on Saturday (February 1, 2014)."
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