What is payjunction and how does it work? PayJunction’s service also includes the ability to generate sales reports as well as search transaction history. Additionally, PayJunction has a PCI-compliant, token-based system that allows merchants to re-charge or refund cards automatically without needing to re-type or re-swipe the card.Does payjunction have merchant complaints? PayJunction has no merchant complaints in the usual online forums; however, there are a handful of negative PayJunction reviews in the comment section of this review. The complaints appear to be isolated incidents based either on a technical issue or merchant confusion.Does paypayjunction have any negative reviews? PayJunction has also received 2 informal reviews on its BBB profile, but it is important to note that these reviews would not be subject to verification by the BBB anyway. One review is positive in tone, while the other is negative. The most recent negative review describes issues with chargebacks:Will changes to my payjunction profile be saved? Changes wont be saved until you sign up for an Enhanced Profile subscription. Founded in 2000 by three UCSB graduates without a single dollar of outside investment, PayJunction has gone from bootstrapped to billions in processing. PayJunction now transacts over $5 billion dollars annually for tens of thousands of users.