Building on 32 years of joint research, the new agreement will see the partners invest up to $AUD41 million across areas of mutual interest.
CSIRO Chief Executive Dr Larry Marshall said the Boeing relationship represented a success story of science partnering with industry to create impact.
"CSIRO has existed for more than 100 years to help industry solve its greatest challenges and create a prosperous society," Dr Marshall said.
"Our partnership with Boeing is a shining example of that, science delivering real solutions for aviation and aerospace industries and creating economic benefits for Australia and jobs for Australians that we know from our history will continue to deliver value for decades.
"The next five years will see our science really move the needle on innovation to create sustainable solutions that deliver the great challenge of lowering emissions while expanding our economy at the same time – but that's what science does."
CSIRO has been named Boeing's Supplier of the year on four occasions: 2011, 2016, 2017 and 2018 in the Environmental category. The parties have made numerous breakthroughs since first partnering in 1989.
These include CSIRO's 'Paintbond' technology, which has been applied to more than a thousand Boeing aeroplanes around the world, saving millions of dollars in maintenance costs.
The chief engineer of The Boeing Company and executive vice president of Boeing Engineering, Test & Technology Greg Hyslop welcomed the partnership.
"Years of research and development is at the core of every critical innovation in aerospace," Mr Hyslop said.
"Our new multi-year agreement with CSIRO will lead to a more sustainable aviation industry, building upon our decades-long partnership that has already produced so many significant advancements for Boeing and our customers."
Over the years the organisations have invested more than $AUD200 million on joint research projects.
The strong relationship with CSIRO was a key factor in Boeing choosing Australia as the location for its largest research and development operation outside the United States.
CSIRO's Chief Technical Advisor to Boeing Shravan Singh said the next few years would see the organisations ramp up projects focused on using AI, machine learning and creating digital twins to improve efficiency and lower costs.
"There is also huge potential to use CSIRO's deep expertise in sustainability to reduce environmental impacts right across the value chain from airplane manufacturing, right through to optimising times around flight operations," Mr Singh said.