The Portuguese manager 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 says 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 forward Cristiano Ronaldo, who played under Mr Mourinho and shares the same agent. 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 international is set to give evidence in his case on 31 July.
Why are Spanish football stars in legal trouble?
Mr Mourinho, 54, is accused of two counts of tax fraud - €1.6m in 2011 and €1.7m in 2012. The Madrid prosecutor says the case was presented to a local court.
Mourinho's major trophies
- Champions League twice, with Porto in 2003-04 and Inter Milan 2009-10
- Premier League three times with Chelsea in 2004-05, 2005-06, 2014-15
- La Liga title with Real Madrid in 2011-2012
Other footballers have been accused of tax fraud in Spain:
- Barcelona and Argentina footballer Lionel Messi was handed a 21-month suspended 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 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