The charges against Shimul and 24 others arrested over a case started at Shahbagh Police Station are under the Anti-Terrorism Act.
Rajib and 13 others are accused in a case lodged with Paltan Police under the Explosives Act.
The courts rejected their bail petitions on Friday evening and remanded them in police custody after hearing police pleas.
The law enforcers arrested Shimul at Bakhshibazar after a special court in the area on Thursday sentenced Khaleda to five years in prison in Zia Orphanage Trust graft case on charges of embezzling Tk 21 million.
Rajib, the head of the BNP’s student affiliate, JCD, was arrested during clashes with police in Naya Paltan after the verdict.
Metropolitan Magistrate Satyabrata Shikder granted the remand of Shimul and two days each for 24 others in the Shabagh police case.
The judge also ordered police to send to jail eight female BNP activists arrested in the case after rejecting both the remand and bail pleas.
In the Explosives Act case, Metropolitan Magistrate Mazharul Islam granted the remand of Rajib and one day each for 13 others.