Representatives from Highland Council along with Scottish economy secretary Keith Brown and UK minister Andrew Dunlop attended the event.
Announced in March last year, the deal involves direct funding and greater borrowing powers.
There has been criticism that the funding package will not benefit the wider Highland area.
The signing ceremony in Invergordon included an agreement to release £12.25m of funding on three projects.
These are the Science Skills Academy STEMD, which is a a network of "science rooms" to promote learning in science and engineering, and the University of the Highlands and Islands' School of Health, Social Care and Life Sciences.
Also, a land remediation project which aims to make vacant land at Inverness' Longman available to businesses.
Other spending planned at a later date includes about £15m to turn Inverness Castle from a criminal and civil courts building into a tourist attraction.

Family and friends of a young couple had hired the boat for an engagement party and were sailing north of Cairo hit was hit, according to eyewitnesses.
An Interior Ministry statement said 15 bodies had been found and six people were still missing.
The captain of the cargo boat has been arrested. Five people were rescued, but at least two children died.
It is not clear if the couple thought to be celebrating their engagement were among the dead, said AFP news agency.
Traffic had been heavy along the Nile, where many Egyptians had been celebrating the end of the holy month of Ramadan.

Sir Nigel dedicated his career to combating human rights violations through his involvement with the United Nations and Amnesty International.
Colleagues described him as "brilliant and unpretentious" and an "inspiring and generous human being".
In 1998 he was knighted for services to human rights and international law.
Sir Nigel worked as a legal adviser at Amnesty International from 1973 onwards and collaborated with universities including the London School of Economics and the University of Essex.
From 1993 to 2001 he served as United Nations Special Rapporteur on Torture.
An international lawyer and professor, Sir Nigel was a prominent member of the UN Human Rights Committee between 2001 and 2016. He served as its chairman from 2012 to 2014.
He helped found the University of Essex Human Rights Centre where staff said he would be greatly missed.
Centre director Dr Clara Sandoval said: "The human rights movement has lost one of its founding fathers.
"The School of Law and the Human Rights Centre have lost a brilliant and unpretentious colleague, an inspiring and generous human being and a wonderful mentor and friend."
University of Essex Vice-Chancellor Professor Anthony Forster added: "Professor Sir Nigel Rodley was a global champion of human rights - writing influential books on international human rights law while also undertaking incredibly important work on behalf of the United Nations.
"He was an inspiration to many, many students and colleagues. Our thoughts are with his family and friends at this time."
Wilder Tayler, secretary general of the International Commission of Jurists, of which Sir Nigel was president, said: "Sir Nigel was a stalwart of the human rights movement.
"His firm commitment to the promotion of human rights and rule of law has had a deep and lasting impact that will continue in his absence."
The £315m Inverness City Region Deal has been formally signed off in a ceremony in Invergordon.
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At least 15 people have been killed in a crash between a cargo vessel and a passenger boat on Egypt's River Nile.
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One of the "founding fathers" of the humans rights movement, Professor Sir Nigel Rodley, has died at the age of 75.