The court ruled against an appeal for her registration by Aldana’s Semilla Party. The case is sent to the Supreme Court now.
Aldana promised that she will continue the fight against corruption. "It has become evident that the fight against corruption and criminal structures in our country has a very high cost," Aldana said in a statement. "I will continue to struggle to transform the country."
"We are surprised by the decision," Ligia Hernandez, the party's deputy secretary and candidate for Congress told Al-Jazeera. "But we respect the decision of the court. This is a big hit to the party, but now we will focus on the campaigns for mayors and congressional representatives."
According to Martin Guzman, the court's secretary, Aldana had failed to meet the requirements of being a candidate.
Guatemalans will go to polls on June 16. If no candidate gets a majority in the first round, a run-off will be on August 11.
Since the announcement of her candidacy, Aldana faced pressures to drop from the race. Rival candidates alleged her of corruption during her period as an attorney general between 2014-2018.
She was living in El Salvador after a warrant was issued for her arrest. The judge who had issued the warrant is undergoing investigation currently for receiving bribes in exchange for the warrant.
Aldana jointly investigated former President Otto Perez Molina with the United Nations-backed International Commission Against Impunity in 2015 which led to the resignation of the president and the then Vice President Roxana Baldetti.
The Constitutional Court will decide Thursday on the candidacy of former first lady Sandra Torres who has been accused of receiving illegal funding during the 2015 presidential race.