The RSF claimed it had "liberated the Sixth Division... and broken the backbone of the Islamic Movement Army," referring to the national army it has been battling since April 2023.
The takeover of the army headquarters could not be independently verified by AFP and the army and its allied forces did not respond to AFP requests for comment.
In a statement, the Popular Resistance -- local fighters allied with the army -- accused the RSF of a "growing media disinformation campaign" aimed at undermining morale and implying that "entering the division headquarters would mean the fall of El-Fasher".
The group said residents were still "resisting in the face of terrorist militias".
Since August, the RSF has intensified artillery and drone attacks on El-Fasher, which has been under siege for more than 18 months.
In recent weeks, the group has captured several parts of the city and overrun nearby displacement camps, eroding the army's last defensive positions.
Drone footage released by the RSF on Sunday appeared to show army vehicles retreating from the army headquarters, while another video showed fighters celebrating next to a sign marked "Sixth Division Infantry".
A third video from the South Darfur capital, Nyala, showed crowds of men on pick-up trucks and tuk-tuks celebrating alongside RSF fighters, honking horns and waving victory signs as women ululated in the streets.
If confirmed, the RSF's claim would mark a major victory for the paramilitaries in Sudan's two-year war, which has killed tens of thousands and displaced nearly 12 million people.
It would also bring under RSF control all five state capitals in the vast Darfur region, where the paramilitary group has established a parallel administration.
About 260,000 civilians -- half of them children -- remain trapped in El-Fasher, cut off from aid and food supplies.
The UN has voiced concern over possible massacres in El-Fasher against non-Arab communities similar to those reported after the RSF captured the nearby Zamzam camp in April.
Analysts also say the RSF advance could leave Sudan effectively partitioned, with the army controlling the north, east and centre, while the RSF dominates Darfur and parts of the south.
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