Berggren has worked in Djurgården for nearly 25 years, of which the last 12 as club director.
Now he takes over the top job in Sef, after the previous general secretary Johan Lindvall was forced out in April.
"Swedish Elite Football has a unique position in society and I look very much forward to continuing to develop Swedish football together with the clubs, the board, our partners and all employees", says Berggren on Sef's website.
"Henrik Berggren has the experience and leadership we need to be able to take the next step in our development. We are convinced that he will contribute to strengthening Swedish elite football on all levels", says Sef's chairman Jens T Andersson.
Berggren will take up the position during the autumn. Until then, vice general secretary Lena Engström will be the acting general secretary.
