It is her first announcement in her new role as "state counsellor", a position similar to prime minister.
She is barred from the presidency but leads the National League for Democracy party which has a huge majority in both houses of parliament.
The move could affect up to 500 prisoners in jail or awaiting trial.
Ms Suu Kyi was once a political prisoner herself, and said the releases were a government priority.
Hundreds have already been freed in recent years as part of the political reform process that ended Myanmar's long period of military rule.
But others have also been arrested, often for holding unauthorised demonstrations.
A government statement did not name who would be freed but there are an estimated 100 political prisoners still in jail and about 400 others, including some students, awaiting trial.
The BBC's Myanmar correspondent, Jonah Fisher, says it is unclear who will qualify as a political prisoner under the announcement, and whether it will apply to Myanmar's many ethnic insurgencies.
US President Barack Obama contacted Ms Suu Kyi and Myanmar's new President, Htin Kyaw, by telephone on Wednesday.
He praised her "determined efforts, over the course of many years and at great personal cost, to achieve a peaceful transfer of power and advance national reconciliation," the White House said.
Also this week Ms Suu Kyi met Chinese Foreign Minister Wang Yi in her capacity as Myanmar's foreign minister.
Aung San Suu Kyi says her new government in Myanmar will work towards freeing all remaining political prisoners within the next two weeks.