Lyons, who was also deputy political editor at the Daily Mirror from 2007-2014, is expected to begin his role in February, overseeing the health service's media and public affairs teams.
He will report to director of comms Simon Enright, who is now the NHS's most senior comms figure following the departure in September of Helen Birtwhistle, who was director of external affairs.
Lyons joins at a time of rising tensions around the nation's health service, with the charity the British Red Cross warning last week of a "humanitarian crisis" within the hospital and ambulance services.
Members of Royal College of Physicians (RCP) have also written to PM Theresa May, arguing that current levels of investment in the NHS are insufficient and are threatening the quality of patient care.
"Our NHS is underfunded, underdoctored and overstretched. The ambulances queuing outside emergency departments are a visual testament to the crisis in social care and the NHS," RCP members said.
May also faced backlash from MPs earlier today at the first Prime Minister's Questions of 2017.
Corbyn asks May if she agrees with the Red Cross that the NHS is facing a "humanitarian crisis". May says that description is "overblown".— Newington (@NewingtonComms) January 11, 2017
Hearing PM rubbish Red Cross claim about state of NHS is shameful. Think they are better placed to say what a humanitarian crisis is #PMQs— Imran Hussain MP (@Imran_HussainMP) January 11, 2017