I think you need to tell your region name where you created your Fargate Profile. In my case, it is working fine.
C:\Users\NADIM AKTHAR\Openstack>aws eks --region ap-southeast-1 update-kubeconfig --name fargate-cluster
Added new context arn:aws:eks:ap-southeast-1:142213003344:cluster/fargate-cluster to C:\Users\NADIM AKTHAR\.kube\config
I hope this will help you.