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.
Other footballers accused of tax fraud in Spain include:
- Barcelona and Argentina footballer Lionel Messi, who has been handed a 21-month jail term. His father Jorge, who manages his finances, was also convicted
- Barcelona defender Javier Mascherano – also an Argentine – admitted tax fraud, escaping a jail term with a one-year suspended sentence
- Barcelona and Brazilian star Neymar is also facing allegations of corruption and fraud over his transfer to the Spanish club in 2013 – a case which also involves his parents. Prosecutors allege the transfer cost much more than publicly declared, and that millions were concealed from authorities
- Former Barcelona president Sandro Rosell, was arrested in May as part of a money-laundering investigation
