During the early part of his career, his research focused on free-radical biology and human disease, and lung damage in premature babies and cystic fibrosis patients.

[6] In 1992, Kelly moved to London and developed a new research interest in the effect of air pollution on lungs and respiratory health.

[8] His current work includes WellHome, a large study of how indoor air pollutants affect childhood asthma in urban environments.

[12] Also that year, he shared the Elsevier Haagen-Smit Prize with Julia Fussell for a paper on the toxicity of particulate air pollution.

[15] Kelly was made a CBE in January 2025 "for services to air pollution research and to human health".