The NSPCC (National Society for the Prevention of Cruelty to Children), Claire House, a children's hospital on the Wirral and Alder Hay hospital each received £250,000 from the Wayne Rooney foundation.
Rooney, 32, made visits to each of the hospitals following the Toffees' win over Swansea City on Monday evening.
Earlier in the year, the striker made a £100,000 donation to the families of the victims of the Manchester Arena bombing.
"As a father, I am horrified that a night out for so many young people could end so tragically," Rooney said in a statement in May.
"My heart goes out all those affected. Please give whatever you can."