Immediately following his doctoral studies, Shepherd took a research position with the Central Electricity Generating Board to study atmospheric physics and air pollution. In 1974, he moved to the Ministry of Agriculture, Fisheries and Food to undertake research into the marine disposal of radioactive waste. In 1976, his research within MAFF changed direction towards mathematical modelling of fishing fleet operations and fish population dynamics, a focus which continued until the 1990s. During 1978–1979, Shepherd first became a visiting researcher at Lamont-Doherty Earth Observatory of Columbia University, a sabbatical activity that he later returned to in 1999. Through the 1980s, he rose through the ranks of MAFF, ultimately reaching the position of Deputy Director in 1989, a role in which he was tasked with the assessment and management of fish stocks, and directly provided advice to MAFF Ministers. During this period, Shepherd also served in a succession of International Council for the Exploration of the Sea working groups and advisory committees on fisheries matters. In 1994, Shepherd left MAFF to become the first Director of the National Oceanography Centre, Southampton, then known as the Southampton Oceanography Centre, in the Hampshirecity of Southampton. The creation of this centre brought together the Natural Environment Research Council's National Institute of Oceanography and the University of Southampton's School of Ocean and Earth Science into a single, purpose-built facility, located within the dock area of the city. During his tenure as Director, 1994–1999, Shepherd served, in part, to bring together these two formerly separate organisations into a single collaborative institution. At the conclusion of his term as Director, Shepherd became Professor of Marine Sciences within the University of Southampton as well as Director of the Earth System Modelling Initiative. From 2006, he assumed a part-time role as a Professorial Research Fellow in Earth System Science at Southampton. In parallel, Shepherd became Deputy Director of the Tyndall Centre for Climate Change Research, and began annual visits to LDEO as an adjunct senior research scientist. Shepherd has served as the member or chair of a number of committees for organisations including NERC, DEFRA, Cefas, DECC and IFREMER. These have largely centred on fisheries, but a number have concerned off-shore operation of oil and gas infrastructures, in particular technology, decommissioning and regulation. Shepherd is a current board member of the Gulf of Mexico Research Initiative, formed in the wake of the Deepwater Horizon oil spill. From 2000 to 2002, Shepherd served as president of the Challenger Society for Marine Science.