Videos posted online on Sunday showed the iconic Greater Nile Petroleum Oil Company Tower engulfed in flames.
“This is truly painful,” said Tagreed Abdin, an architect of the building, in a post on Twitter.
Air strikes and ground battles have continued in Khartoum and other towns and cities since fighting broke out in April.
Over one million people have been forced to flee the country, the UN has said.
Located near the River Nile, the 18-storey oil firm skyscraper is one of the most recognisable landmarks in Khartoum.
Ms Abdin said it defined the skyline of the city, and lamented “such senseless destruction”.
I’ve been out of the loop with what’s happening in Africa in the past few years. Why there are so many coups happening in Africa recently? What changes that trigger all these coups?