He worked as a professor of physics at the University of Colorado Boulder from 1898 to 1907. He spent a one-year sabbatical with Pierre and Marie Curie in their radium research laboratory at the University of Paris in 1906 and was then invited to work with them from 1907 to 1912. He published 17 scientific papers during this time mostly around the properties of X-rays from radioactive sources and the measurement of heat generated from radioactive disintegration.  Although none of the papers were in direct collaboration with the Curies, he worked closely with them and it was reported that when Marie Curie visited America years later, she stated that she most wanted to see "Niagara Falls, The Grand Canyon and William Duane"
Duane refined a technique for extracting radon-222 gas from radium sulfate solutions. Solutions containing 1 gram of radium were "milked" to create radon "seeds" of about 20 millicuries each.  These "seeds" were distributed throughout Paris for use in endocurietherapy. Duane perfected this "milking" technique during his time in Paris and referred to the device as a "radium cow".
He returned to the United States in 1913 and worked in a joint role as assistant professor of physics at Harvard and Research Fellow in Physics of the Harvard Cancer Commission. The Cancer Commission was founded in 1901 and hired Duane to investigate the usage of radium emanations in the treatment of cancer. In 1915 he built Boston's first "radium cow" and thousands of patients were treated with the radon-222 generated from it. He published eight papers on the technical details of using radioactive material and X-Rays in the treatment of cancer. In 1917, Harvard created the chair of bio-physics for him.
Duane made important contributions to the technical details of measuring X-ray dosage in terms of the ionization of air. He conducted research to determine the structure of matter and on the mechanism of radiation. He developed the Duane-Hunt law, relating the minimum wavelength of X-rays to the threshold voltage of the cathode rays  that excite them; and Duane's hypothesis of quantized translative momentum transfer.
In 1925, Arthur Compton demonstrated that the scattering of 130,000-volt X-rays from the first sixteen elements in the periodic table (hydrogen through sulfur) were polarized. Duane spearheaded an effort to prove that Compton's interpretation of the Compton effect was wrong. Duane carried out a series of experiments to disprove Compton, but instead found evidence that Compton was correct. In 1924, Duane conceded that this was the case.
He served as councillor of the Societe de Physique from 1920 to 1923, as chairman of the division of physical sciences of the National Research Council from 1922 to 1923, as president of the Society for Cancer Research in 1923 and as vice president of section B of the American Association for the Advancement of Science from 1927 to 1928.
After his retirement from Harvard in 1934, he was awarded the title professor of biophysics emeritus.