Pyrethroid-based insecticides are widely used in malaria and arbovirus control. However, growing pyrethroid resistance is compromising effectiveness, posing a significant public health threat. Chlorfenapyr, a novel pyrrole pro-insecticide, has been introduced to target pyrethroid-resistant mosquitoes due to its unique mode of action. It is activated by oxidases, which are protective against pyrethroids, and the oxidated compound inhibits the mitochondrial electron transport chain. To explore the relationship between pyrethroid resistance and chlorfenapyr efficacy, we conducted a series of experiments with pyrethroid resistant Aedes aegypti and Anopheles gambiae with the objective of informing future vector management strategies. Pyrethroid resistant Anopheles gambiae Siaya strain from western Kenya were exposed to a chlorfenapyr dose of 40µg or 60µg every generation or every other generation respectively for six selections over a span of seven months. Resistance to chlorfenapyr and permethrin was compared between the selected and the unselected strains. We observed a significant increase in survival of the selected strain to low doses of chlorfenapyr with no change in the levels of permethrin resistance. We also examined the impact of sub-lethal chlorfenapyr exposure on fecundity and development. We observed no significant differences in overall fecundity between the exposed and unexposed mosquitoes, however there were slight changes at different developmental stages. Finally, we utilized RNA sequencing to determine transcriptional changes associated with chlorfenapyr exposure at different time points. Taken together, these studies explore the complicated mode of action of chlorfenapyr, the long-term effects of utilizing chlorfenapyr in pyrethroid resistant populations and the potential for cross resistance.