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Freelancers don't have to pay income tax on foreign remittance in Pakistan. However, the income must come as remittance through proper banking channels.
It means that if the income is transferred through local bank (usually done when you withdraw using Payoneer) then it won't be tax exempt.
As far as NTN registration and filing tax return is concerned, you should talk to a tax consultant who deals specifically in this category for freelancers in Pakistan.
You have to submit your file return and if you are running an IT company without registration with FBR and other relevant boards then it is an illegal attempt.
Since you have tax exception as an IT company so it is recommended that you register yourself to avail this benefit.
As per Tax Exemptions clause # 133 of Income tax ordinance 2001, which was amended in 2017, there is an exemption for exports of software or IT services or IT enabled services till 30th June, 2019 as long as 80% of the income comes via banking channels.
You can download PDF of FBR and read this ordinance on page # 453-454.
Discussion on Tax and Freelancing: You can also find here several discussions on tax and freelancing topic from other freelancers.
FBR Tax Return Guideline: Join this group on Facebook to post your questions or issues.
You may also refer to question on @Quora: What rate of tax do freelancers in Pakistan have to pay?