Portuguese-born Mourinho is accused of defrauding Spain of €3.3m (£2.9m; $3.6m) in taxes between 2011 and 2012. He has yet to comment on the claim.
A prosecutor said he did not declare income from the use of his image rights in order to get an "illicit benefit".
Other big names in football have been accused of tax fraud in Spain recently.
Those include Real Madrid star Cristiano Ronaldo, who played under Mourinho and shares the same agent as him. The player is accused of defrauding tax authorities of €14.7m, by also hiding his income from image rights.
He denies the accusations and is threatening to leave Spain. The Portuguese-born star is set to give evidence in his case on 31 July.
Mourinho, 54, is accused of two counts of tax fraud - €1.6m in 2011 and €1.7m in 2012. The Madrid prosecutor said the case was presented to a local court.
Mourinho accused of tax fraud during Real Madrid stint
20 June 2017
Read: 953
Manchester United manager Jose Mourinho has been accused of tax fraud by Spanish prosecutors investigating his time as Real Madrid's head coach.
