It is the first time it has suffered a deficit since 2001 with Wood - who took over in 2007 - helping to deliver 14 successive years of profit before quitting in January.
However, 2016’s figures showed a profit of just £6,000, down from £201,000 in 2015 and £295,000 in 2014.
Last year’s was always likely to fall further after it was decided they would revalue one of their assets - Odsal Stadium.
That has been reduced by almost £400,000 “in line with required accounting practices” while a lack of any home internationals and also sending two teams to the World Cup in Australia also incurred large costs.
The RFL did add, though, it is “budgeted to return its planned significant surplus in 2018.”
The full statement read: “The Rugby Football League can confirm that it will report a loss of £2.029 million for last year (2017).
“A loss was budgeted for and approved by the Rugby Football League as it recognised 2017 would be a difficult financial year but that it would need to continue to invest in a number of areas.
“Significant investment was made in the International set up to maximise the opportunity of a World Cup on home soil in 2021, in off field systems and infrastructure to benefit the entire game, whilst there was also significant funds provided though Sport England and invested directly into frontline programme delivery to boost participation.
“A year in which England also had no home international fixtures, 2017 saw significant investment to give all national programmes the best chance of success on the international stage.
“An effective and widely commended England Unit was created, a successful and valuable mid-season test against Samoa completed and the England Men’s Senior Team reached the final of the World Cup, narrowly losing to hosts Australia in the final.
“The year end result also reflects an increased focus in transforming the sport off the field with significant investment in technology and systems that bring the vast majority of operations online, best placed for the future and ready to make returns on that investment from 2018 onwards.
“Following its 2017 settlement and a change in Sport England’s funding strategy, the Rugby Football League reduced the funding of back office costs and increased funding directly into frontline programme delivery by £670,000 to support increased participation in the sport.
“The 2017 loss includes all costs incurred by the Rugby Football League following a restructure of its Senior Executive team and following a reduction in the valuation of Odsal Stadium by almost £400,000, in line with required accounting practices.
“With a home series against New Zealand in the autumn of 2018 and improved commercial deals secured in the first quarter of this year, the Rugby Football League is budgeted to return its planned significant surplus in 2018.”
The annual accounts will be published in full later this year following approval by the Rugby Football League Council while Wood's replacement is also expected to be announced later this month.
Ralph Rimmer has been operating as interim chief executive since February and hopes to claim the role himself.