Malaria remains a major public health threat in Burkina Faso, as in most sub-Saharan Africa countries. Malaria control relies mainly on long-lasting insecticide-treated nets (LLINs) and indoor residual spraying. In Burkina Faso, an escalating of insecticide resistance has been observed over the last decades. This study aimed to investigate insecticide resistance and the underlying mechanisms in Anopheles gambiae complex in Ouagadougou. Anopheles gambiae s.l. larvae were collected from gutters and ponds, in Zogona, Tampouy and Tanghin, 3 localities in Ouagadougou from July to October 2018. The larvae were reared in the laboratory to adults stage and susceptibility profile to pyrethroid, carbamate, and organophosphate insecticides was assessed using WHO tube assays. Mosquito species and mutations linked with insecticide resistance, were identified through PCR. More than 95% of the collected An. gambiae s.l. were An. arabiensis. An. arabiensis displayed high resistance to permethrin and deltamethrin, with mortalities below 30%, but was fully susceptible to bendiocarb, fenitrothion, and malathion. A high-frequency of the pyrethroid resistance-associated kdr mutation 1014F (0.81) was recorded, while the frequency of 1014S mutation (0.18) was lower. However, the carbamate and organophosphate-associated Ace-1 119S mutation was not detected. Localities and breeding site type appear to influence pyrethroid resistance in the An. arabiensis population of Ouagadougou. The high resistance to pyrethroids in An. arabiensis of urban Ouagadougou is underpinned, at least in part by high-frequency kdr mutations. This result supports the switch to next-generation LLINs, in well-established pyrethroid resistance zones of Burkina Faso including Ouagadougout