AIFF general secretary, Kushal Das, after consultation with executive committee members on Thursday, decided to hand offer the job to Medeira, who has been working as deputy to former coaches Bob Houghton and Armando Colaco for the past three years.
The post had fallen vacant after interim coach, Armando Colaco, rejected the AIFF's offer to extend his contract by one year.
The AIFF had tried to rope in Salgaocar Sports Club coach, Karim Bencherifa for the top post, but he too refused citing club commitments.
"Its a great honour to be India's coach. But at the same time, its a huge responsibility as well," the 46-year-old Medeira said.
Asked whether he will continue with the same support staff and preparatory camps, the former India midfielder said he will meet Das on Monday in Delhi to sort out the things.
"I have asked Marcus Pacheco (the current goalkeeping coach) to be the assistant coach besides looking after goalkeeping. The support staff will remain the same," he added.
Medeira said his immediate concern was the three upcoming international friendlies, against Malaysia on November 13 and 16 in Assam and Kolkata respectively, and against Zambia on November 29 in Goa.
"Given the tight schedule of the I-League, we are expected to have a one day camp prior to our first friendly. I hope we do well," he said.
The biggest challenge, though, will be the SAFF Cup when India defend their title, which they won with a reserve side in Bangladesh, at home in December, he added.