Boban, 47, will oversee the "football pillar" of FIFA's new administration, focussing on developing the game and the organisation of competitions, FIFA said in a statement.
Marco Villiger, currently FIFA's legal director, was named as the other deputy secretary general and will be in charge of commercial and administrative operations.
The appointments were announced by FIFA's new secretary general Fatma Samoura who confirmed the decision to split the administration of the sport's governing body into two halves.
Samoura, the first woman to hold the position, was addressing FIFA employees for the first time since her surprise appointment earlier this month.
The event was not open to the media, although FIFA said the Senegalese, who previously had a long career with the United Nations but has no experience in football administration, delivered an "inspiring" speech.
Boban made 51 appearances for Croatia and captained the side which finished third at the 1998 World Cup, their best-ever performance.
He also won four Serie A titles and the Champions League during a nine-year spell with AC Milan. Recently, he has been working as a television commentator in Croatia and Italy.
CORRUPTION SCANDAL
Football's world ruling body has been embroiled in a corruption scandal over the past year and several dozen officials, including former FIFA executive committee members, have been indicted in the United States.
So far, at least 15 people and two corporate entities have pleaded guilty in the U.S. cases.
Last week, Markus Kattner was fired as deputy secretary general after FIFA said that an internal investigation had "uncovered breaches of his fiduciary responsibilities in connection with his employment contact."
Samoura said her priority would be to oversees reforms which were passed in February and which FIFA says will avoid a repeat of the previous scandals.
“It is my goal to keep on putting the reforms into action and to help FIFA in its process of being recognised as an institution that is run under the principles of good governance, and one that people may be proud of,” she said.
However, FIFA has been plunged into fresh controversy following a resolution passed by the Congress in Mexico City on May 13 which gives the FIFA Council the power to dismiss members of its watchdog committees.
Domenico Scala, a Swiss businessman who led reforms, quit his post as head of the audit and compliance committee, saying his body had lost its independence.
(Writing by Brian Homewood, editing by Ken Ferris and Ed Osmond)
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