On Wednesday, he signed a contract in Brussels following lengthy talks.
"The contract was signed at the residence of the (Iranian) ambassador between Mr. Wilmots and Mehdi Taj (the president of the Iranian football federation)," a diplomat at the embassy told AFP by telephone.
The former Belgian striker had travelled to Iran earlier this month and was expected to sign a $1.2 million (1 million euros) a year deal in Tehran.
However, the 50-year-old who was capped 70 times for his country returned to Belgium with no agreement.
Iranian news reports said the delay was caused by difficulties involved with "banking transfers."
The diplomat confirmed that the contract runs until the end of the 2022 World Cup in Qatar.
Wilmots takes over from Portuguese coach Carlos Queiroz who stepped down after eight years in charge in January following Iran's semi-final exit in the Asian Cup when they went down 3-0 to Japan.
He led Iran to two World Cup finals and extended his contract to 2019 after the 2018 tournament in Russia.