Thompson is the fourth MLA to be handed the portfolio since Paul Okalik became premier in 1999.
Kilabuk will now take over as minister of Culture, Language, Elders and Youth and Community Government and Transportation.
Olayuk Akesuk will retain his post as minister of Sustainable Development.
The premier made the announcement at a press briefing on Friday, saying the shuffle was made to help spread the workload.
"Minister Kilabuk has agreed, he is willing and wanting to assume the responsibility and help this government to fulfil its responsibility of the Bathurst Mandate and keep Inuit Qaujimajatuqangit on the agenda," said Okalik.
Kilabuk said despite the shuffle he is honoured and feels privileged to be a cabinet member.
"It's an honour to be able to serve in any capacity I can," he said.
He noted, however, that he did not ask for a change in portfolio but said he would still honour and respect the premier's decision.
As for Kilabuk's replacement, Manitok Thompson, Okalik said he is confident in her abilities to continue curriculum development and future trades programs.
Nonetheless, the government still faces the daunting task of revamping Bill 1, the failed Education Act, which the legislative assembly rejected two weeks ago. The problem will likely carry over to the next government.
With an election less than a year away the shuffle came as a surprise, but Okalik said the rationale is to get as much done in the next 11 months as possible.
At the same time, due to the short schedule, Okalik said he wants to keep portfolio changes to a minimum.
Civil service shifts
Changes were not limited to ministerial positions a number of civil service postings were also affected.
One of the more significant moves includes -- Pam Hine, who will take over as deputy minister of education, while handing over the presidency of the Nunavut Housing Corporation to Peter Scott.
Anne Crawford, secretary to cabinet and deputy minister to Executive and Intergovernmental Affairs is leaving her job too. She will take over as deputy minister of health and social services on an interim basis.