The 56-year-old is accused of committing tax fraud in 2011 and 2012 when he coached Spanish giants Real Madrid.
According to the agreement seen by AFP, Mourinho accepted a one-year jail sentence immediately commuted to a fine of 182,500 euros.
The Portuguese coach will also have to pay an additional penalty of 1.98 million euros ($2.3 million).
Mourinho, sacked by Manchester United in December following a string of disappointing performances, is the latest high-profile football figure to be judged over his tax affairs in Spain.
Spanish prosecutors accuse Mourinho, who coached Real Madrid between 2010 and 2013, of failing to declare income of 1.6 million euros in 2011 and 1.7 million euros in 2012.
The grounds for the case, as with a series of football stars based in Spain, is how income from Mourinho's image rights was managed and declared.
Prosecutors believe by ceding his image rights to a series of companies based in tax havens, Mourinho committed fraud by not declaring the income those companies made from his image rights.