The loss adds to a $9.2m deficit posted for 2023, when the Wallabies crashed out of the World Cup in France at the group stage, and outstrips the $27.1m shortfall for 2020 during the depths of the COVID-19 pandemic.
Despite the red ink, the governing body was positive about the outlook and said it was now positioned to retain the "full up-side" of this year's British and Irish Lions tour and the coming 2027 World Cup on home soil.
"Rugby Australia made great progress in 2024 towards building a sustainable, thriving model for Australian Rugby," CEO Phil Waugh said in a statement.
"There is still much to do but the pathway to a prosperous future is clear."
RA said it spent more than $10 million integrating the ACT Brumbies and NSW Waratahs under its management and more than $5 million on the voluntary administration and exit of the Melbourne Rebels.
More than $9 million was paid to service an $80 million loan taken out with a private lender in 2023.
Waugh said RA was forecasting a record surplus in 2025 on the back of the Lions tour, which should give it the option of exiting the loan.
The governing body then enters a new broadcasting deal with Nine Entertainment from 2026 on better terms than the previous deal.