Dougherty won the 2008 Hughes Medal of the Royal Society "for innovative use of magnetic field data that led to discovery of an atmosphere around one of Saturn's moons and the way it revolutionised our view of the role of planetary moons in the Solar System". She was the second woman ever to receive such an accolade, 102 years after Hertha Ayrton in 1906. Dougherty was elected a Fellow of the Royal Society in 2012 and was recognized by the UK Science Council as one of the 100 top UK living scientists. She was awarded a prestigious Royal Society Research Professorship in 2014. Dougherty was awarded the Gold Medal of the Royal Astronomical Society for geophysics in 2017, the fifth woman ever to receive the honour. Dougherty has contributed significantly to the UK space sector, and chaired the Science Programme Advisory Committee of the UK Space Agency between 2014 and 2016. She was made Commander of the Order of the British Empire (CBE) in the 2018 New Year Honours for "services to UK Physical Science Research". Dougherty won the 2018 Richard Glazebrook Medal and Prize from the Institute of Physics. In 2019 Dougherty was named a Fellow of the American Geophysical Union.