Following his PhD, John Hardy did postdoctoral research at the MRC Neuropathogenesis Unit in Newcastle-upon-Tyne and further postdoctoral work at the Swedish Brain Bank where he worked on Alzheimer's disease.

He became Assistant Professor of Biochemistry at St. Mary's Hospital, Imperial College London in 1985 and initiated genetic studies of Alzheimer's disease. He became Associate Professor in 1989 taking the Pfeiffer Endowed Chair of Alzheimer's Research at the University of South Florida in 1992. In 1996 he moved to Mayo Clinic Jacksonville as Consultant and Professor of Neuroscience.

He became Chair of Neuroscience in 2000 and moved to NIA, Bethesda as Chief of the Laboratory of Neurogenetics in 2001. In 2007 he took up the Chair of Molecular Biology of Neurological Disease at the Reta Lila Weston Institute of Neurological Studies, UCL.

In 2015, he was awarded the Breakthrough Prize, and, in 2018, the Brain Prize from The Lundbeck Foundation in Denmark.