The technical meaning of pruning someone or something by the TVA would be resetting it, or in practice sending it to the Void. However, in context of the sentence it doesn't really matter. Sylvie is getting Loki to shut up so she can continue her life's mission, the exact terminology she uses here doesn't really matter. Her point is she was taken from her timeline, her home, and it was destroyed.
Sylvie: Loki, shut up. I was pruned before you even existed. I have been waiting for this moment my entire life. I just need a second to get my head straight, okay?
Loki, Season 1 Episode 6, "For All Time, Always"
On top of that, as FuzzyBoots points out her timeline was pruned. They "reset" it when they take Sylvie away. So whilst she was not physically pruned herself her home was and the TVA would have pruned her if she didn't escape. Ever since then they have been trying to prune her, her whole life. So whilst she might not be technically correct in saying she was pruned for the purpose of the conversation and for the overall meaning as it applies to her it's pretty accurate and doesn't matter that much.