Mr Scott will start his new role on July 19, in time for semester two.

He takes over from interim vice-chancellor Stephen Garton, who will revert to his role as senior deputy vice-chancellor.

Prior to Prof Garton, Michael Spence served in the university's vice-chancellor role for 12 years, leaving in early 2021 to join University College London.

Mr Scott will earn a base salary of $840,000 per year, and could earn up to $1.15 million each year if he obtains all available bonuses.

He has signed up for a five-year term.

"The University of Sydney, Australia's first university, was created because our founders recognised the importance of education in driving societal change and it is that mission I am looking forward to supporting," Mr Scott said.

"I want our staff and students to know how valued they are and I look forward to working closely with them and with industry, community and government to secure our future and solve the world's most pressing challenges."

The Australian tertiary education sector cut thousands of jobs amid the COVID-19 pandemic and has warned more job losses are likely.

Universities were effectively excluded from receiving the federal government's JobKeeper wage subsidy scheme, which will end in a fortnight, and were also hit by international students being unable to enter Australia.

NSW Education Minister Sarah Mitchell congratulated Mr Scott and said he'd remain as departmental secretary until the end of April.

"Mark has been outstanding in his efforts as secretary of the Department of Education. He has played a key role in helping the government undertake the biggest reforms to education in NSW in a generation," Ms Mitchell said.

Current group deputy secretary Georgina Harrisson will be appointed acting secretary until a permanent replacement for Mr Scott is secured.

Australian Associated Press