Sir Keith Burnett, who retired in September from the University of Sheffield after ten years, had a total remuneration package of £456,000 - making him the tenth highest paid vice chancellor in the country.
Second highest paid was Bob Cryan, of Huddersfield University, whose basic salary was £326,000, a total of £385,000, including pension, according to data from the Office for Students.
He was followed by Sir Alan Langlands, whose basic salary was £281,000 (total £294,000 including pension).
The data also shows that nearly 300 senior staff at Yorkshire universities were paid over £100,000 - 117 of them at Leeds University, and another 67 at Sheffield.
Altogether, 124 of the 133 universities across England paid their heads more than the £150,000 the Prime Minister earns.
Nicola Dandridge, chief executive of the OfS, said it was not for them to set pay, but where pay was out of kilter, or salary increases at the top outstripped pay awards to other staff, vice chancellros should be prepared to answer “tough questions.”
She said: “It is good to see signs of pay restraint at some universities, with some vice chancellors refusing a salary increase.”
She added that institutions receive significant funding, both in the form of direct grants drawn from public taxation as well as funding from student loans.
“Universities - and individual vice chancellors - need to be confident that they can justify the pay that they receive,” said Ms Dandridge.
However, the report was criticised by the University and College Union (UCU), which branded the OfS a “paper tiger”.
The union said the report failed to look at the excessive and arbitrary rises still enjoyed by some vice chancellors, or tackle the expenses and other benefits in kind that have “plagued universities in recent years”.
UCU head of policy Matt Waddup said: “The report simply regurgitates some of the analysis done by UCU and others in recent years, but pulls its punches on how to address the problem.
“The OfS fails to ask why some vice chancellors are still picking up double-digit pay rises and doesn’t even look at their expenses or other benefits in kind.
“This report sends a message that those who accept such largesse have nothing to fear from the new regulator.”
Education Secretary Damian Hinds said: “We set up the Office for Students to look out for students’ interests and it is absolutely right that the OfS demands greater transparency from universities by requiring them to justify the pay and benefits of their vice chancellors.
“We have given the OfS powers to take action if universities do not do this and we expect them to be used where necessary.”
Sheffield University’s new vice chancellor is Prof Koen Lamberts, formerly VC of York University, who started in November and whose salary has been agreed at £285,000.
Huddersfield University said Prof Cryan had been a "remarkably effective and inspirational leader" and the university was "one of the most financially secure in the UK’s Higher Education sector."
A spokesman said: "His salary is reviewed each year by a committee of members of the Governing Council of the University; he is not a member of this committee, nor in attendance at its meeting.”
Leeds University said as Yorkshire’s largest university they inevitably employed a lot of people, providing 38,000 students “with an exceptional education.”
Sir Alan's total remuneration was below the sector average for vice chancellors and he had only had one pay increase of 1.1 per cent since 2013.
The seven highest vice-chancellor basic salaries for 2017/18 in Yorkshire:
University of Sheffield, £346,000
University of Huddersfield, £326,000
University of Leeds, £281,000
University of York £254,000
University of Hull £248,000
Sheffield Hallam £240,000
Leeds Beckett University £226,000
Top 7 pay packages in 2017/18
University of Sheffield, £456,000
University of Huddersfield £385,000
University of York £323,000
University of Leeds, £294,000
Sheffield Hallam £281,000
Leeds Beckett University £263,000
University of Hull £261,000