Along with three others, Drogba submitted papers to stand in the polls earlier this month.
The FIF’s Electoral Commission ruled that the former Chelsea striker did not fulfil its long list of eligibility criteria.
His bid was rejected as two of the names he had submitted as his sponsors were ruled not to have the necessary authority to do so.
Officials from the Ivorian club Africa Sport and a body representing referees, AMAF-CI, had also backed the federation’s current first vice-president Sory Diabate.
Different officials from the same organisations had also signed Drogba’s papers, with the FIF’s commission ruling they were not authorised to do so.
In the case of Africa Sports, a sporting club in Ivory Coast, the head of its football section had given his approval to Drogba while the chairman of the whole club had backed Diabate.
It meant that Drogba only had the backing of two top-flight Ivorian clubs and not the three that FIF statutes demand.
The rejection will come as a bitter blow to football fans in Ivory Coast, thousands of whom had come out to support him earlier this month when he submitted his bid to stand.
Drogba played more than 100 times for the Elephants including at the 2006 and 2010 World Cups, and as well as Chelsea he played for French giants Marseille, Chinese club Shanghai Shenhua and Galatasaray in Turkey.
An application for Paul Koffi Kouadio was also rejected, leaving Diabate and Yacine Idriss Diallo, a former FIF third vice-president, as the remaining candidates.
Drogba and Kouadio both now have five days to appeal against the decision.