The 48-year-old Bosnian joins on a two-year deal, with the option of a further 12 months, after the Tigers agreed a settlement with Turkish side Kayserispor.
Jakirovic had only been in Turkey since January, having previously led Dinamo Zagreb to qualification for the Champions League, and succeeds Ruben Selles, who was dismissed last month after Hull narrowly avoided relegation from the Championship.
Hull were briefly linked with former Boro boss Tony Mowbray after Selles’ sacking.
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Chairman Acun Ilicali said on wearehullcity.co.uk: “We are delighted to secure the services of Sergej.
“We believe in the football that he will bring to the MKM Stadium for us and, importantly, he has proven himself to be a winner throughout his career.
“My dream for our club has never changed from the first day I took over, and I believe in Sergej as we look forward to the 2025/26 Sky Bet Championship campaign together as one family.”
Jakirovic’s backroom team of Marko Salatovic, Marin Ivancic and Andjelo Roguljic join him in moving from Kayserispor, while first-team coach Andy Dawson and goalkeeping coach Erbil Bozkurt remain on the staff.
A former midfielder and Bosnia international, Jakirovic began his managerial career with Sesvete in the Croatian second tier before moving on to Gorica, Maribor, Zrinjski Mostar and Rijeka.
Hull finished the season in 21st place in the Championship, staying up at the expense of Luton on goal difference.
