Bulatovic, 53, from Montenegro, died late on Friday in the emergency hospital in Belgrade, the Beta news agency reported on Saturday.
He had suffered serious brain damage after the shooting earlier in the day, it said.
The federation cancelled all football games scheduled to take place over the weekend.
Bulatovic, the federation's secretary-general, was shot by an unknown assailant in the entrance of his office in central Belgrade on Friday morning.
Federation employees heard a gunshot and found Bulatovic slumped in the foyer of the office. The attacker escaped.
Assassinations are common in
the former Yugoslavia
Serbian Interior Minister Dragan Jocic told state television on Friday that police had made an identikit picture of the assassin and were investigating possible motives for the murder.
"[We have] never been the target of threats and nothing led us to expect such an event," said Nikola Jockovic, a senior official at the Serbian Football Federation, on Friday.
Bulatovic, a law graduate, played for the Buducnost club in the Montenegrin capital Podgorica in the 1960s and later became its director.
He held senior roles in the Serbia-Montenegro Football Federation, formerly called the Yugoslav Football Federation, since the late 1980s.
Serbia and Montenegro formed a loose union a year ago to replace the rump Yugoslavia. They were the only republics left in Yugoslavia after the other Balkan republics broke away.
The 53-year-old Montenegrin lawyer had held the post for the past 13 years.