In 2015 a government committee blocked the assets of the former player for Cairo-based club Al-Ahly and Egypt's national team, two years after he retired.
On Tuesday an administrative court reversed the decision, one of the judges, who did not want to be named, told AFP.
Aboutrika, one of the most successful African footballers of his generation, had publicly endorsed the presidential bid of the Muslim Brotherhood's Mohamed Morsi in 2012.
Morsi went on to become Egypt's first democratically elected president, only for the army to oust him one year later and ban the Brotherhood as a "terrorist" organisation.
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Aboutrika's lawyer, Mohamed Osmane, confirmed Tuesday's decision to AFP, saying the freeze had included "all of his assets, bank accounts, properties".
The authorities can appeal the latest decision, he added.
In May 2015, Aboutrika's share certificates in the Tours travel company were seized over accusations it had funded the Brotherhood since December 2013.
In an interview with state-run Al-Ahram newspaper in May last year, Aboutrika denied that his company -- or any of his partners -- had ever funded the Islamist movement.
Since Morsi's overthrow, a police crackdown against the Brotherhood has left hundreds dead and thousands jailed.
Aboutrika retired in 2013, and the 37-year-old has since avoided expressing his political views publicly.