The figures, which were revealed in accounts for the 12 months to September 30, lay bare the pummelling the bank has taken this year with statutory pre-tax losses coming in at £614 million following £737m of loan impairments.
Clydesdale had previously revealed it made a £183m pre-tax operating loss on an accounting basis that excluded a number of non-cash items.
Mr Thorburn was chief operating officer of Clydesdale, which is owned by National Australia Bank, until July 2011 when he replaced Lynne Peacock.
His earnings for the 2012 financial year are one-third of the £1.5m banked by Ms Peacock for working nine months of 2011, though her package included a £475,000 termination payment.
In that year Mr Thorburn received £1.2m, most of it from incentive schemes.
In fact, for the 2012 financial year Mr Thorburn was not the bank's highest paid employee.
John Hooper, an executive responsible for back-office services, received £918,000, 80% more than Mr Thorburn. Before joining Clydesdale in 2009 Mr Hooper used to run NAB's global institutional business (nabCapital). His current basic salary is £703,000, topped up with £214,000 of benefits and allowances.
Mr Thorburn, has a £400,000 basic package and receives £109,000 of benefits.
It is further evidence of how the role of chief executive has changed.
In July NAB chief executive Cameron Clyne became executive chairman of Clydesdale, in place of non-executive Sir Malcolm Williamson.
A Clydesdale spokesman said: "Directors' remuneration is very closely linked to business performance and we've been clear that's not where it needs to be. As a result, no annual pay rises will be awarded to the senior management team in the year ahead.
"Given the significant challenges facing our business, it is also only right that no STI (short-term incentive) bonus payments were awarded to directors for the past financial year."