The boy was 13 when he killed eight girls, a boy and a school guard at Vladislav Ribnikar school in Belgrade in 2023.
The project would have built on the ruins of the defence ministry bombed by Nato back in 1999.
The president's son-in-law wants to build a hotel on the ruins of the former Yugoslav Army headquarters.
President Aleksandar Vucic - populist and close to Russia - has faced months of protests and alleges a foreign coup plot.
The Serbian project, led by Trump's son-in-law Jared Kushner, has run into opposition and scandal.
Serbian officials have denied allegations security forces deployed a military-grade Long Range Acoustic Device.
The collapse of a station canopy that killed 15 people has galvanised anger towards the government.
Police gather evidence against MPs who let off smoke bombs and flares in a protest over claims of corruption.
Milos Vucevic's resignation follows months of nationwide demonstrations over the collapse of a station roof which killed 15.
