The move comes two days after gunmen opened fire at an Ivory Coast beach resort killing 18 people, including four French citizens.
Al-Qaeda in the Islamic Maghreb (AQIM) said it carried out the assault.
Militants have also launched attacks in Burkina Faso and Mali recently.
French Interior Minister Bernard Cazeneuve made the announcement on a visit to Abidjan to show France’s support for Ivory Coast. He was joined by Foreign Minister Jean-Marc Ayrault.
There, they visited some of the wounded from Sunday’s attack on the Grand-Bassam resort, the first jihadist attack in Ivory Coast and the third in the region since November.
“The desire to position this (gendarmerie) team in Ouagadougou is to enable us to immediately dispense advice and co-ordinate other actions in the event of a terrorist crisis,” Mr Cazeneuve said.
France has about 3,500 troops to combat militants across the Sahel region. Its Operation Barkhane succeeded Operation Serval, launched in 2013 to oust extremists from northern Mali.
AQIM threatened France and its allies in Mali, saying they would “receive a response”, with their “criminal leaders” and interests targeted.
The al-Qaeda linked group has also claimed two other similar attacks – an assault on a cafe and a hotel in Burkina Faso in January that killed 30 people, and a hostage siege at a hotel in Mali in November that left 30 dead.