Linsi, who has been acting as interim general secretary since the summer, was given unanimous backing during the Executive Committee meeting held in Madrid this morning.
He filled the gap left by Michel Zen-Ruffinen who left FIFA following the World Cup.
Zen-Ruffinen left under a cloud after a bitter battle with FIFA president Sepp Blatter leading up to the presidential elections in May.
Said Blatter: "I am delighted that the Executive Committee has concurred with my proposal and confirmed Urs Linsi in the role of FIFA general secretary.
"Over the last six months, he has proven his ability, not only in his expert area of finance, but also in his efforts to restructure the FIFA general secretariat."
Added Linsi: "I would like to thank the president and the FIFA Executive Committee for this vote of confidence. I will do everything in my power to ensure that FIFA continues to move in the direction already agreed upon by FIFA’s competent bodies."
