We're US-based, mostly processing payments via checks. A client based in Pakistan needs to make a payment by credit card (visa) for our services. I thought about using PayPal, but when testing it out, Pakistan is not on the country pop-up list for sending payment.

Does Paypal not permit payments from Pakistan?

Would we have any problems accepting payment from this client by going with our own merchant account and a payment processor?

I think Stormpay might work in your situation.

Goodluck

Paypal coverage is not international see some threads of this forum and you will find only few countries are on paypal list.

you can use other payment processors or use WU, Wire.