Over his 26-year career at the BBC, Boothman has worked in various senior roles within news and current affairs, most recently on political programme production at the Scottish Parliament.
He won the Royal Television Society's 'Scoop of the Year' prize last year as producer of the story detailing the release of Lockerbie bomber Abdelbasset al-Megrahi.
In 2009, Boothman was the executive producer of the BAFTA Scotland-nominated documentary Wasted Nation, along with its debate programme.
He has overseen coverage of four Scottish elections, three general elections and two European Parliament elections, along with annual coverage of Scottish party political conferences.
Boothman takes over from Atholl Duncan, who left BBC Scotland in April to become executive director UK and global for accountancy body ICAS.
"This is a hugely interesting time for news and current affairs in Scotland and I'm looking forward to ensuring that BBC Scotland continues to deliver it across all our platforms and for all our audiences," said Boothman.
BBC Scotland director Ken MacQuarrie described Boothman as a journalist of integrity and great experience. He added: "I know under John, BBC Scotland News and Current Affairs will continue to lead the field in the provision of breaking news and analysis."
Also welcoming the appointment, the director of BBC News Helen Boaden said: "John is a very experienced journalist with a superb track record. He has a deep understanding of audiences in Scotland and will bring great skill and passion to this role."
Yesterday, it was reported that BBC News is poised to make major cuts to its 8,000 employees in the UK and abroad, as part of plans to secure annual savings of 20% to its budget.
Former BBC foreign correspondent Martin Bell told the corporation to save money by stopping the "expensive and wasteful practice" of sending lead presenters to the scene of international incidents.