Not sure if this will work for others. I had the same problem and managed to solve it.
My store is new and got my first sale via paypal and it was marked as payment pending. Was like this for a day.
Did some research, found that email conflicts within Paypal could be an issue.
I have one email I use to log into Shopify and a different email for Paypal.
I logged into my Paypal, added/linked the email address I use to log into Shopify. I then made it my primary email on Paypal.
I went back into Shopify, deactivated my paypal and then reactivated using the new primary email (same email I log into Shopify).
'Payment Pending' disappeared and the money then instantly showed up in my paypal.
Hope this helps someone