Kaan Ayhan scored on the final kick of the match, and Turkey beat the United States 3-2 Thursday night for its only win of the World Cup.
The referee was "determined to be inadmissible due to vetting concerns and was denied entry," a U.S. Customs and Border Protection spokesperson said, without going into further detail.
Iran's World Cup team arrived in Mexico wearing lapel pins highlighting the victims of a deadly missile strike on an elementary school at the start of the war in the Mideast.
Secretary of State Marco Rubio indicated last week the Trump administration had "no problem" with providing visas to Iran's team.
High temperatures could be in place in several of the host cities during the World Cup.
The final World Cup roster for the U.S. Men's National Team is set, with only a couple weeks left before the tournament gets underway.