The Oscar-nominated actor, director and screenwriter is being recognised for his services to drama and to the community of Northern Ireland.
The 51-year-old said: "I feel humble, elated, and incredibly lucky."
Speaking from Pinewood Studios, where he is preparing his new film, he said: "When I was a kid I dreamed of pulling on a shirt for the Northern Ireland football team.
"I could only imagine how proud you might feel. Today it feels like they just gave me the shirt, and my heart's fit to burst."
Earlier this year, he won praises for his portrayal of Sir Laurence Olivier, to whose career Branagh's has often been compared, in My Week With Marilyn.
He was nominated for an Oscar and a Bafta for the role.
A total of 86 people from Northern Ireland are on the Queen's birthday honours list this year, including a former Commonwealth pole vault champion.
Mike Bull, 65, from Bangor, has been awarded the OBE for services to sport and charity.
He attracted audiences of hundreds of shipyard workers on their lunch break as a student in the 1960s, practising in a shed under the shadow of the Harland and Wolff's crane.
BBC broadcaster Wendy Austin was awarded an MBE.
So too was Heather Monteverde of Macmillan Cancer support - she was recognised for 25 years of service to those battling the illness.
"During that time I have met so many really inspirational people, patients, families and carers, and some really amazing colleagues working across health and social care," she said.
"It has been a wonderful experience, a career I have absolutely loved and continue to love and feel very privileged to have had."
Joan Burney-Keatings was one of the youngest honour recipients at age 37.
She received the MBE for services to the arts in her role as chief executive of the Cinemagic International Film and Television Festival for Young People.
"I'm still in a bit of a state of shock," she said.
"Just really, really humbled and overwhelmed. This award is for so many other people, my family, husband and children, and all the amazing people I work with at Cinemagic."
Among the CBEs were former director of the National Trust in Northern Ireland Ruth Laird for public and voluntary service, Leonard O'Hagan, chairman of Belfast Harbour Commissioners for services to the ports industry and Elaine Way, chief executive of the Western Health Trust for services to healthcare.
OBEs included Norman Apsley, chief executive of the Northern Ireland Science Park.
Also among the MBEs are Robert Arnott, founder member of the Northern Ireland Kidney Research Fund and Transplant Games for services to kidney research and Ian Bothwell, founder of the Crossfire Trust, for services to the community in South Armagh.
The oldest recipient, Jean Rea aged 89, was given a medal of the Order of the British Empire for Meritorious Service.
Northern Ireland 2012 honours list in full:
Knights Bachelor (KCB): Mr Kenneth Charles Branagh.
Companions of the Order of the Bath (CB): Mr Edgar Frederick Jardine, Mr Alan David Shannon.
Commanders of the Order of the British Empire (CBE): Mrs Ruth Laird, Dr Leonard John Patrick O'Hagan DL, Mrs Elaine June Way.
Officers of the Order of the British Empire (OBE): Dr Norman Apsley, Dr Olive Buckley, Dr Michael Anthony Bull, Miss Bridget Josephine Glendinning, Mr John Alexander Graham, Mr Brendan Michael McCartan, Dr Bhaskar Sengupta, Mr Edward Vernon.
Members of the Order of the British Empire (MBE): Mrs Joanne Elizabeth Andrew-Steer, Mr Robert Arnott, Mr John Alfred Best, Mr Ian James Bothwell, Mrs Margaret Irene Boyd, Mr Raymond Patrick Boyle, Mrs Joan Burney-Keatings, Mrs Joan Carmichael, Mrs Jean Gibson, Mr Thomas Gilpin, Mr Trevor Alexander Hassin, Mr Robert Jonathan Hegan, Dr Wendy Elizabeth Austin Hewitt, Mr Patrick Robert William Hurst, Mrs Eleanore Margaret Huston, Mr Brendan Johnston, Mr Leslie Jones, Mrs Adele Margretta Kerr, Miss Helen Kirkpatrick, Mr James Leitch, Mrs Jean Liddell, Mr Reginald James Magowan, Mr Henry (Harry) McCullough, Mr Roger George McCune, Mr Robert Joseph McFerran, Mrs Clare McGartland, Mr James Brian McGookin, Mr Malachy Vincent McGreevy, Mrs Ann McGregor-Sistern, Mrs Margaret Jane McMullen, Mrs Heather Monteverde, Mr Robert David Morrow, Mrs Marian Anne Moutray, Mr Francis Joseph O'Hagan, Mrs Catherine Joy Peters, Mr Henry Joseph Quinn, Mr Trevor Quinn, Mr John Calvert Gingles Rodgers, Mrs Susan Fullerton Semple, Mr Ivor Robert Stevenson.
British Empire Medal (BEM): Mrs Myrtle Cecilia Moore Allen, Mr Samuel Ronald Martin Bothwell JP, Mrs Edith Eleanor Boyd, Mr William John Davis, Mr John Bryan Dunlop, Mr James David Elliott, Mrs Anna Marie Hamilton, Mrs Elizabeth Henry, Mrs Elaine Herd, Mrs Margaret Hunter, Miss Irene Kerr, Mr William James Lunn, Mrs Carolyn McCabe, Mr Nelson Samuel McGonagle, Mr Paul McKee, Mr Philip Jude McKeown, Mrs Elizabeth Millar, Mrs Isobel Parke, Mr William David Pollock, Mrs Bertha Ann Rankin, Miss Jean Rea, Mrs Irene Rebecca Audrey Robb, Mrs Elizabeth Rose, Mrs Patricia Ann Shannon, Miss Anne Skelton Vance, Mrs Margaret Wilson, Mrs Isabella Woods, Mr Robert Dawson Wright.
Queen's Police Medal (QPM): Mr Kenneth Annett, Mr Stephen McQueen, Mr Derek Harry Scott.
Queen's Ambulance Service Medal (QASM): Mr Brian McNeill.