"The (Malian Armed Forces) took up position in the town of Kidal this Tuesday," the general staff said in a statement on social media.
The move marks a notable symbolic success for Mali's ruling junta, which seized power in 2020.
The army and the state had been virtually absent for years from the town, which is controlled by the predominantly Tuareg armed groups.
The insubordination of the town and of the Kidal region, where the army suffered humiliating defeats between 2012 and 2014, has been a long-standing source of irritation for the government in the capital, Bamako.
Mali's military leaders have made the restoration of territorial sovereignty their mantra.
The military had drawn closer to Kidal over the weekend, clashing with separatist fighters and rebel groups in what may have signaled the start of fighting for the strategically important northern crossroads.
The rebels in Kidal on Friday cut telephone links in anticipation of an army offensive following several days of air strikes.
Some 25,000 people live in the Kidal desert area, a key site on the road to Algeria and a historic hotbed of insurrection.
Violence has escalated in the north since August, with the military, rebels and jihadists vying for control as the U.N. mission, MINUSMA, evacuates its camps, triggering a race to seize territory.
The rebels do not want the peacekeepers to hand their camps back to the Malian army, saying it would contravene previously agreed ceasefire and peace deals struck with the government.
The army on October 2 dispatched a large convoy towards Kidal in anticipation of the U.N.'s departure.
But U.N. forces, citing the "deteriorating security situation" and threats to its peacekeepers, accelerated their pull-out, upsetting the ruling junta, which wanted the departure to coincide with the army's arrival.
Instead, when the mission left the Kidal camp on October 31, the rebels immediately seized control.
The Tuaregs previously launched an insurgency in 2012, inflicting humiliating defeats on the army before agreeing to a ceasefire in 2014 and a peace deal in 2015.
The uprising in 2012 coincided with insurgencies by radical Islamist groups who have never stopped fighting Bamako, plunging Mali into a political, security and humanitarian crisis that has spread to neighbouring Burkina Faso and Niger.
Since July, the U.N. mission has withdrawn nearly 6,000 civilian and uniformed personnel, after the ruling junta demanded the mission depart from Mali.
The deadline for withdrawal, set by the U.N. Security Council, is December 31.