She served as a bacteriologist during World War I, and was the third scientist and the first woman appointed to work at the Walter and Eliza Hall Institute of Medical Research after its establishment in 1915.

In December 1909, Williams took up a position as nurse inspector with the Unley Local Board of Health for which she undertook home visits and tested patients for diphtheria, measles, and other notifiable diseases.

[2] After the outbreak of World War I in 1914, Eleanor Williams was invited by Dr Trent Champion de Crespigny to join him on active service with the First Australian Imperial Force.

[3] Infectious disease was emerging as a significant issue for the campaign in Turkey and the Middle East, and the army wanted to recruit people with bacteriological and laboratory training to work on the problem.

[6][7][8] She continued to work with Martin throughout the war, on a variety of infectious diseases, including meningitis, streptococci, staphylococci, gas gangrene, and epidemic influenza.

[citation needed] Following her repatriation in 1919, Eleanor Williams moved to Melbourne, and was appointed to the position of 'second assistant' at the newly-established Walter and Eliza Hall Institute of Medical Research by director Sydney Patterson.

[5][9] In the early 1920s, the Institute's focus was on respiratory and intestinal infections, and Williams worked on pneumonia, syphilis and dysentery, as well as the serological diagnosis of hydatid tapeworms.

While her lack of academic qualifications prevented her from lecturing at the University of Melbourne, she established and led the Institute's Diagnostic Microbiology Laboratory, and attended international and national conferences where she presented papers in her own right.

In the first decade of the service, laboratory tests were carried out at the Walter and Eliza Hall Institute of Medical Research, under the supervision of Williams and her colleague Dr Ian Wood.

[12] She was recognised with an obituary in The Medical Journal of Australia, written by Frank Macfarlane Burnet and Dr Ian Wood, which spoke of her 'remarkable knowledge, keen sense of humour, and tenacity of purpose'.