"No to the settlement," protesters chanted, heading toward the presidential palace in the capital Khartoum.
Near-weekly protests have rocked Sudan since army chief Abdel Fattah al-Burhan led an October 2021 military coup derailing a transition to civilian rule.
On December 5, military leaders and multiple civilian factions signed the deal as the first component of a planned two-phase political process.
Last week's deal was signed by Burhan and his deputy Mohamed Hamdan Daglo as well as civilian groups including the Forces for Freedom and Change, which was ousted in last year's coup.
During the signing ceremony, Burhan vowed that the military would "go back to the barracks".
Civilian and military signatories to the deal have pledged to hammer out the details of transitional justice, accountability and security reform "within weeks".
But critics have slammed the deal, which largely fell short on specifics and timelines, as "vague" and "opaque".
"We are against this deal, which doesn't provide any clarity regarding our demands of justice and accountability," said Nisreen, a 38-year-old protester in Khartoum.
"We no longer trust the military. We gave them the trust once before and they later launched the coup."
Sudan's short-lived transition was installed following the 2019 ouster of president Omar al-Bashir.