The military was the final Turkish institution where women were prohibited from wearing the headscarf, after reforms by the Islamic-rooted government under President Recep Tayyip Erdogan that has allowed it to be worn in education, politics and the police.
The move, ordered by the defence ministry, applies to female officers working in the general staff and command headquarters and branches, the state-run Anadolu news agency said.
"The problem with preventing the wearing of the headscarf has now been completely removed in Turkey," Defence Minister Fikri Isik was quoted as saying by Anadolu.
"Those who wish can perform their duties while wearing the headscarf. The gendarmerie and the police lifted this restriction and now the army has."
According to the reform, women may wear the headscarf underneath their cap or beret so long as it is the same colour as their uniform and does not cover their faces.
The reform, announced just under two months before Turkey votes in a crucial referendum on expanding Erdogan's powers, will come into force once it is published in the official gazette.
It will also apply to female cadets, but it was not immediately clear if it applies to women on combat missions.
The ruling Islamic-rooted Justice and Development Party (AKP), co-founded by Erdogan, has long pressed for the removal of restrictions on women wearing the headscarf.
Speaking to Turkish reporters at his offices in Ankara, Prime Minister Binali Yildirim said he believed the removal of the ban was "very positive", pro-government daily Yeni Safak said.
- Army last holdout -
The military has usually been seen as the strongest bastion of secular Turkey and had been traditionally hostile to any perceived Islamisation of state institutions.
But its political power has ebbed after the government increased control over the armed forces following a failed military coup in July, blamed on followers of US-based Islamic preacher Fethullah Gulen.
Turkey lifted a ban on the wearing of the Muslim headscarf, known as the hijab, on university campuses in 2010.
It allowed female students to wear the headscarf in state institutions from 2013 and in high schools in 2014.
Female MPs meanwhile began to wear headscarves in parliament from October 2013 when four female AKP lawmakers wore the hijab in a session, in contrast to the scenes in 1999 when a headscarf-wearing MP from the now defunct Virtue Party was heckled out of the chamber.
Famously, the choosing of AKP co-founder Abdullah Gul as president in 2007 caused a political crisis as his wife wears the hijab -- a controversy unthinkable when Erdogan took the top office in 2014. His wife Emine also wears the headscarf.
And in the latest key reform before the army's move, Turkey in August allowed policewomen to wear the headscarf as part of their uniform.
At the time of controversy over lifting the ban in the police forces, pro-government media pointed out that several Western states had already granted female officers permission to wear the garment.
The military was until now seen as the last holdout on the issue, although civilians employed by the armed forces have been able to wear the hijab since last year.
There had been signs that the landmark reform was in the offing when press reports said that a woman, Merve Gurbuz, was undergoing training that could make her Turkey's first hijab-wearing fighter pilot.
Highlighting the sensitivity of the issue, Turkish media seized heavily on recent reports that US actress Lindsay Lohan -- who has met Erdogan and shown interest in Islam -- was asked to take off her headscarf at London's Heathrow Airport.
Erdogan's critics have long accused the president of eating away at the secular pillars of modern Turkey as set up by its founder Mustafa Kemal Ataturk when he established the Turkish republic in 1923.
The government rejects the suggestions, saying it allows freedom of worship for all Turkish citizens whatever their beliefs.
