The 55-year-old Hanoi native takes over following an irregular meeting of the city People’s Council, the legislature, on Friday morning.
Anh, who has a PhD in physics, won a unanimous vote one week after he was appointed deputy Communist Party chief of the capital.
Accepting the position, he said he "is deeply aware that this is a great honor but also a heavy responsibility."
He said Hanoi has to focus on key tasks and feasible solutions to both achieve comprehensive and sustainable development and promote the cultural values of a city that is 1,010 years old.
"I will proactively work closely with all units, listen to the voices of the people as well as the businesses to innovate and complete the mode of leadership, direction and administration," he said.
Luu Binh Nhuong, lawmaker and deputy head of the National Assembly's Committee for People's Aspirations, said before the appointment meeting that Hanoi's new chairman has an important role in setting up policies for finding and keeping talented people.
"We hope the new chairman could come up with good strategies to find talented people who are capable of planning long-term strategies for development and ensure those with good qualities are not missed or lost," Lao Dong newspaper quoted him as saying.
Anh was a lecturer at the Institute of Engineering Physics, Hanoi University of Science and Technology, from 1988 to 1995 before moving to the technology ministry’s Research Institute of Posts and Telecommunications and then its State Agency for Technology Innovation.
His stint in politics began when he became deputy Party chief of Phu Tho Province near Hanoi and then the province's chairman from May 2013 to September 2015.
He then became deputy minister and, in April 2016, Minister of Science and Technology.
In the last five years technology has contributed greatly to Vietnam's socio-economic development, demonstrated by improvements in the quality of growth and exports of technology products accounting for nearly half of Vietnam's exports.
As a science minister, Anh highly evaluated science and technology achievement of Hanoi, noting that Hoa Lac Hi-Tech Park in Thach That District is now the cradle of typical models in the field, leading the country in the science and technology development.
The Friday meeting also saw the house dismiss Chung as city chairman.
Chung, 53, was suspended last month before being arrested pending investigation into his involvement in three criminal cases.
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