All three of Iran's group games are in the US, but the players and support staff have been told they have to fly in and out of the country on match day.
Iran says 15 other officials and support staff have been denied visas altogether, which an official has described as political interference in sport in its worst form.
The World Cup, jointly hosted by the US, Canada and Mexico, begins on 11 June, with Iran securing their place by finishing top of their qualification group in March 2025, almost a year before the US and Israel began attacks on the country.
This will be the first iteration of the World Cup to see a host nation receive the team of a country it is at war with.
The Iranian team landed in Tijuana early on Sunday morning local time. They will be based there after relocating the training base from the American city of Tucson, Arizona, in late May.
US officials said visas had been issued to all players and "necessary support staff" on Friday, 10 days before Iran's opening fixture against New Zealand in Los Angeles on 15 June.
According to Iranian state-linked media, 15 officials including the football federation chief, his deputy, and a media director are among those denied entry to the US.
US officials said that Iran would not be allowed to "abuse this system to sneak terrorists into the United States under false pretences", echoing comments US Secretary of State Marco Rubio made earlier in the week in which he said the Iranian delegation would not be allowed to include people with links to the Islamic Revolutionary Guards Corps - a powerful branch of the Iranian armed forces.
Several players in the Iranian squad have completed mandatory military service with the group.
Iran's embassy in Turkey accused the US of "politically biased interference in sport" by denying visas to a "large portion of the managerial and executive staff" and "technical advisers".
Embassy officials also called on Fifa, football's world governing body, to intervene on the visa row.Iran are also due to play Belgium in California and Egypt in Seattle in their other two group games.