Arroyo, who became leader in 2001 after a popular uprising that removed her predecessor, Joseph Estrada, cannot stand for the presidency again, but she hopes to wield power as speaker of the House of Representatives.
As speaker she would have the power to initiate impeachment proceedings against the president as well as block the administration's legislative agenda.
Arroyo's critics also fear the move is part of a plan to change the constitution and install her as prime minister by 2016.
Jose Midas Marquez, spokesman for the court, said justices voted unanimously to dismiss a petition from a left-wing lawmaker to reverse an earlier ruling by the election agency allowing Arroyo to run for a congressional seat.
Marquez said there was no law prohibiting Arroyo from running for a congressional seat.
Arroyo faces scant opposition for a congressional seat from her province of Pampanga, and is almost assured of becoming the next leader of the lower house, which is dominated by her political allies.
