Importar can be translated as "to import" and "to matter". To import has the meaning of bringing something from another place and it is usually an economic ideia. Think about ordering something from another country on eBay. That is "importar" in the "to import" sense.
When you want to say that something makes no difference, then "importar" means "to matter". For example, you could translate the sentence "não importa o que você pensa" as "it doesn't matter what you think".
In the sentence"não importa quando você vem", you should translate as "it doesn't matter", but a better translation would be "you can come whenever you want".