When we meet the younger Nick Fury in Captain Marvel, he is just a “lowly desk jockey” who still has two working eyes, but hasn’t had any experience yet with aliens threats.
Granted, previous MCU movies and TV shows that there have been instances of alien and extraterrestrial objects making their way to Earth, but as Samuel L. Jackson informed EW, Fury will face an uphill battle in Captain Marvel convincing his superiors that they need to be preparing for these extraordinary forces, both from beyond our world and those that surface close to home.
We know this will pave the way for him setting up the Avengers Initiative, but at this point, humanity as a whole is still close to two decades away from learning that aliens exist.
We’ll have to wait and see how exactly Fury meets Carol Danvers, but his encounter with her will lead to him realize that there are other people like her with special powers/abilities, and that they can be an asset.