The star of Wonders of the Universe receives the Michael Faraday Prize in the Royal Society's 2012 Awards, Medals and Prize Lectures.
Another University of Manchester academic, Professor David Leigh FRS, has been selected to give the Bakerian Lecture – one of the most highly regarded lectures in Physical Sciences.
The lecture, which is accompanied by a medal and a gift of £1,000, is delivered annually and is one of the oldest scientific lectures in the world – first given in 1775.
Professor Cox has become one of the most recognised figures in science and has won plaudits for making science accessible to a wider audience.
His latest BBC series, Wonders of Life, will be aired later this year. He has described it as "a physicist's take" on natural history and the story of life and has been filmed in some of the most spectacular locations from around the globe.
A graduate of the University, Professor Cox – along with thousands of other scientists – works on the Large Hadron Collider at CERN, and contributed to research which resulted in the recent discovery of the Higgs Boson.
He also is a prominent and passionate champion of science in the media.
Professor Leigh recently made the move to Manchester to take up a position as Professor of Organic Chemistry. He is a world leader in the field of synthetic molecular motors, machines and nanotechnology.
He has previously received many international prizes and awards for his work, including the EU Descartes Prize for Research and the US Feynman Prize for Nanotechnology, both in 2007. He was elected Fellow of the Royal Society in 2009.
Speaking about the Bakerian Lecture and his work at Manchester, Professor Leigh said: "It's great when our group's work is recognised by prizes, of course.
"The Bakerian Lecture is one of the premier awards of the Royal Society and I was both surprised and honoured when the Royal Society asked me to give the 2013 Lecture."
Professor Leigh, who began his career at UMIST in the 1990's, also spoke about returning to Manchester.
He said: "Ever since it was announced that I was moving back to Manchester I've been overwhelmed by the warmth and generosity of everyone in the School of Chemistry. The willingness of everyone to put up with the inconvenience of the building work while our labs are being refurbished, for example, has been really important for us."
Sir Paul Nurse, President of the Royal Society, said: "The recipients of the Society's awards and medals this year represent the best of the best in science yet again. Science can improve our health and quality of life, help solve the world's biggest problems, and support sustainability.
"These outstanding scientists work across a range of disciplines and their research could have real impact. We're very pleased to be able to recognise them in this way and highlight the important work they are doing."
The full list of recipients of Awards, Medals and Prize Lectures for 2012 is available at http://royalsociety.org/news/top-scientists-2012/