[15]: 61  Shortly after this, Payne-Scott joined AWA, a prominent electronics manufacturer and operator of two-way radio communications systems in Australia.

[11]: 31 On 18 August 1941, Payne-Scott joined the Radiophysics Laboratory of the Australian government's Commonwealth Scientific and Industrial Research Organisation (CSIRO).

During World War II, she was engaged in top secret work investigating radar technology, becoming Australia's expert on the detection of aircraft using Plan Position Indicator (PPI) displays.

[11]: 60 As the focus of the Radiophysics Lab switched from developing radar systems to repurposing them for scientific pursuits, she was a major contributor to setting new goals.

[17] In December 1945, she authored a summary of "all knowledge available and measurements taken" at the Radiophysics Lab, and suggested future research directions that "set the thinking" for the group.

[11]: 171 In 1951, Payne-Scott's scientific career ended abruptly, with her decision to resign in order to start a family; at the time, there was no maternity leave.

[21] In 1951 – just a few months before her son, Peter Gavin Hall, was born – Payne-Scott resigned her post due to there being no maternity leave available at the time.

[22] In 2018, The New York Times wrote a belated obituary for her, detailing how her work helped lay the foundation for a new field of science called radio astronomy.

[11]: 7 Danebank School, where she taught after her radio astronomy career, hosts an annual Ruby Payne-Scott Lecture "presented by outstanding women scientists in a variety of fields".