Metropolitan Magistrate Md Maruf Hossain passed the order on Tuesday afternoon, rejecting his bail plea.
Earlier in the day, the BNP spokesperson surrendered before the lower court in line with the Supreme Court order.
On Monday, the apex court ordered Mirza Fakhrul to surrender before a trial court by Tuesday.
The court also ordered to dispose a High Court ruling over the senior BNP leader’s bail within two weeks.
The four-member bench of the Appellate Division, led by Chief Justice Surendra Kumar Sinha, issued the order after rejecting three petitions filed by Fakhrul seeking extension of his bail in the cases filed with Paltan and Motijheel police stations last year and this year.