The United States striker signed a pre-contract agreement with Stoke in August and was due to move to England at the start of this month when his New England Revolution contract expired.
However, Stoke boss Mark Hughes was thwarted in his attempt to bring in Agudelo when the 21-year-old was refused a work permit in November.
Agudelo is still ineligible to play for Stoke, who must wait four months from their original work permit application before they are able to reapply for a permit.
That has not stopped them from going through with the deal, but for the meantime the highly-rated frontman will ply his trade with Utrecht.
Stoke chief executive Tony Scholes said: "We were surprised and bitterly disappointed when our application for a work permit was rejected by the appeals panel - as were many other people in the game.
"It's still our view that Juan is a great talent and is a player that Mark Hughes would like to join our squad. We have therefore decided that we are going to reapply for a work permit at the earliest opportunity.
"We have signed Juan but he cannot play in this country, so we're loaning him out to Utrecht to allow him to not only develop his experience of playing in Europe but also to stay match sharp.
"Hopefully we will be successful with our second work permit application and Juan will be able to join Mark's squad in advance of next season."
Agudelo already has 17 international caps to his name and will be hoping to feature in this year’s FIFA World Cup.
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