The new deal comes despite an inconsistent World Cup qualifying campaign when they memorably beat group winners Russia at home but lost on their travels to Luxembourg and Azerbaijan.
They finished fifth in the six-team group, with one win, four draws and five defeats.
"When I was appointed Northern Ireland manager I was honoured to have been chosen to manage my country; and I am extremely happy to have agreed a new two year deal with the Irish Football Association," O'Neill said.
"I have said all along that I would like to continue in the role - I think there has been a major transition in the team; it's a very young squad, but a squad which has developed during the last campaign, with several young players of quality emerging; and I am now looking forward to taking the team into the European Championship qualifiers."
(Writing by Kieran Barry, editing by Justin Palmer)
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