call me up
call me
Call someone up, call someone (when both mean phone someone)
Any subtle differences when you're using them?

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Hi, no, there's not much difference in meaning...they both mean the same thing. But call me up is maybe a tiny bit more casual.

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“Call me up” seems less common and might be more used if there is some doubt. As an imperative, I think “call me” is better. 
I wonder if I should call my old girlfriend up?
Why don’t you just call him up and let him know how interested you are?