Larkin worked in science communication for three years after her PhD. In 2003 Larkin joined the Tyndall Centre working on conflicts between climate change and policy. She is interested in ways that research can inform policy decisions. She became part of the team at Manchester, developing the energy scenario tool ASK in 2005, which allowed them to build low-carbon energy scenarios. She works on carbon budgets and cumulative emissions. She was involved in the creation of the Climate Change Act 2008. She was appointed a lecturer in 2008 and became Director of the Tyndall Centre in 2013. She remains as a member of the Tyndall Centre council. In 2013 she called for more radical strategies to tackle climate change. She became a Professor at the University of Manchester in 2015. She is part of the University Living Lab. She delivered a Ted Talk in 2015 entitled Climate Change is Happening, Here's How We Adapt. The talk considered the reality of climate change and the fate of a world where wealthy nations do not take any responsibility. It was described as the 'best human rights talk of the year' by City Atlas: New Haven. She also spoke at TEDxYouth@Manchester in 2015 and New Scientist live. In 2016 Larkin was awarded the Researcher of the Year by University of Manchester. Larkin is interested in energy systems and international transport. She provided expert-witness to the trial of the Heathrow 13, protestors from the Plane Stupid campaign group, who chained themselves to Heathrow Airport's Northern Runway to protest against the impact of climate change. She avoids flying as she believes that climate change experts should act as role models in curbing aviation growth. In 2017 she was made Head of the School of Mechanical, Aerospace and Civil Engineering at the University of Manchester, and in 2019 became Head of the School of Engineering. She has spoken extensively about climate change in mainstream media. She appeared on the podcast Introductions Necessary. She investigates the impact of the Paris Agreement for big-emitting nations.
Larkin is principal investigator for the EPSRC project Stepping Up. The project looks for integrated solutions to future challenges in food, water and energy. She studied the emissions associated with the future global wheat demand. It combines anaerobic digestion, using insect protein for animal feed, recovery of the value of waste and ways to use surplus food from waste streams. Her research has been funded by the EPSRC and the Economic and Social Research Council.