Anas Haqqani was arrested late Tuesday along with Hafiz Rashid, another commander, by the National Directorate of Security (NDS), the Afghan intelligence agency officials said, according to Dawn online.
"We hope that these two arrests will have direct consequences on the network and their centre of command," NDS spokesman Haseeb Sediqi said.
Anas played an important role in the network's "strategic decision-making" and frequently travelled to Gulf states to get funding, Sediqi said.
The Haqqanis have been blamed for spectacular attacks on the Afghan government and NATO forces' targets across Afghanistan as well as for kidnappings and murders.
The Haqqani network was founded by Jalaluddin Haqqani, an Afghan guerrilla leader bankrolled by the US to fight Soviet troops in Afghanistan in 1980s.