Land Forces commander Hulusi Akar, 63, takes over as chief of staff from retiring General Necdet Ozel as part of a major shake-up of the army's top brass.
His appointment was made during a three-day annual meeting of the Supreme Military Council headed by Prime Minister Ahmet Davutoglu.
Akar, who has extensive NATO experience, is seen as more hawkish than Ozel, whose leadership coincided with a period of relative peace in the Turkey's Kurdish-dominated southeast.
Ankara has launched a two-pronged "anti-terror" offensive against jihadists in Syria and PKK militants in northern Iraq after a series of attacks on Turkish soil, including a suicide bombing blamed on IS that killed 32 pro-Kurdish activists in the town of Suruc last month.
The PKK, which accuses the government of collaborating with IS, shot dead two Turkish police in reprisal for the Suruc attack, kick starting a wave of violence that has shattered a 2013 ceasefire between rebels and the state.
According to an AFP toll, 20 members of the Turkish security forces have since died in attacks blamed on the PKK.
The overhaul in the army command also comes as Turkey continues to redefine the role of the military, whose political influence has waned since the ruling Justice and Development Party (AKP) of President Recep Tayyip Erdogan took power in 2002.
But Erdogan's Islamic-rooted AKP has clipped its wings through a series of trials, which have been criticised by rights groups.
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