The Ottoman Empire era of rule in Bosnia (first as a sanjak, then as an eyalet) and Herzegovina (also as a sanjak, then eyalet) lasted from 1463/1482 to 1908.

The Ottoman conquest of Bosnia and Herzegovina started in 1384, and subsequently the Ottoman invasion expanded into the so-called Bosansko Krajište. The Kingdom of Bosnia finally fell in 1463. Herzegovina fell to the Turks in 1482. It took another century for the western parts of today's Bosnia to succumb to Ottoman attacks. Bosnia continued legally under the royal House of Berislavić, and fell finally in 1527 with the fall of its capital Jajce. The first occupation administration was established that same year.

A significant number of Bosnians converted to Islam after the conquest by the Ottoman Empire in the second half of the 15th century, giving it a unique character within the Balkan region. This conversion appears to have been not sudden but a gradual process based on various rules imposed by the Ottomans — it took more than a hundred years for the number of Muslims to become the majority religion. The general view among scholars is that the Islamization of the Bosnian population was not the result of violent methods of conversions but was, for the most part, peaceful and voluntary.

The Turks had conquered Slavonia and most of Hungary by 1541. In the next century, most of the Bosnian province wasn't a borderland and developed in relative peace. It was administered by the Ottoman Bosnia Eyalet and Herzegovina Eyalet.

However, when the Empire lost the war of 1683–1697 with Austria, and ceded Slavonia and Hungary to Austria at the Treaty of Karlowitz, Bosnia's northern and western borders became the frontier between the Austrian and Ottoman empires.

In 1716, Austria occupied northern Bosnia and northern Serbia, but this lasted only until 1739 when they were ceded to the Ottoman Empire at the Treaty of Belgrade. The borders set then remained in place for another century and a half, though the border wars continued.

The wars between the Ottomans and Austria and Venice impoverished Bosnia, and encouraged further migration and resettlement; Muslim refugees from Hungary and Slavonia resettled in Bosnia, assimilating into the native Bosniak population, whilst many Eastern Orthodox Christians, mostly from Kosovo but also including those from Serbia and Bosnia, resettled across the Bosnian border in Slavonia and the Military Frontier at the invitation of the Austrian Emperor.

According to an Ottoman Muslim account of the Austro-Russian–Turkish War (1735–39) translated into English by C. Fraser, Bosnian Muslim women fought in battle since they "acquired the courage of heroes" against the Austrian Germans at the siege of Osterwitch-atyk (Östroviç-i âtık) fortress. Bosnian Muslim women and men were among the casualties during the Battle of Osterwitchatyk. Bosnian Muslim women fought in the defense of the fortress of Būzin (Büzin). Women and men resisted the Austrians at the Chetin (Çetin) Fortress. The women of the Bosnians were deemed to be militaristic according to non-Ottoman records of the war between the Ottomans and Austrians and they played a role in the Bosnian success in battle against the Austrian attackers. Yeni Pazar, Izvornik, Östroviç-i âtık, Çetin, Būzin, Gradişka, and Banaluka were struck by the Austrians. A French account described the bravery in battle of Bosnian Muslim women who fought in the war.