Running payroll for the first time as a Pakistani business needs more setup than most founders expect. NTN, bank arrangements, EOBI registration, tax compliance, payroll software, and the first pay cycle itself. Skip a step and you build up a compliance backlog that comes back to bite you later. Here is the order we recommend to founders.

Step 1: Get your business registrations right (Week 1-2)

NTN (FBR registration): mandatory before paying anyone. Apply via FBR IRIS or your tax practitioner.
Sales Tax Registration, if applicable to your business model
Provincial Shops & Establishments registration in the province where you operate
SECP company registration (if a registered company)

Step 2: Open a business bank account

Salary disbursement comes from a corporate account, not the founder's personal. The bank can also set up a payroll services arrangement (bulk credit to employee accounts, often discounted fees).

Step 3: Register with EOBI (if employing 5+)

If you employ 5 or more workers (within EOBI insurable categories), EOBI registration is required. You apply online, get an employer registration number, and each employee is given a PI number. See: EOBI guide.

Step 4: Register with provincial social security

Depending on your province:

Punjab: PESSI (see the PESSI guide)
Sindh: SESSI
KPK: KPESSI
Balochistan: BESSI

Step 5: Pick payroll software (do not start with Excel)

Starting with Excel "to keep things simple" is the most common first-payroll mistake. By month 6 you have separate Excel files for attendance, leave, deductions and advances, and none of them agree with each other. Pick payroll software from day 1.

What to look for: Pakistani compliance built-in (EOBI, PESSI, FBR WHT, tax slabs, professional tax), per-employee monthly pricing, mobile app, dual currency if relevant. See: small-business payroll buyer guide.

Step 6: Configure your payroll software

Company details (NTN, EOBI registration, provincial SS, address)
Pay cycle (monthly typically, end of month)
Working hours (typically 9-to-5 or 9-to-6)
Leave types (CL 10, SL 8-16, AL 14, maternity, paternity)
Overtime rates (working / non-working / gazetted multipliers)
EOBI rate (current notification)
Provincial SS rate (current notification)
Tax slabs (current FBR notification)
Approval workflow (who approves payroll for disbursement)

Step 7: Add your first employees

Per employee:

Name, CNIC, joining date, designation, department
Salary breakdown (basic, allowances)
Bank account for salary credit
EOBI PI number (after EOBI registration)
Provincial SS number (after registration)
Tax filing status (filer / non-filer)
Emergency contact

Step 8: Set up attendance from day 1

Even if you have 3 employees today, set up attendance properly. Face recognition on mobile is the cheapest and quickest option. See: face attendance setup.

Step 9: Run a test payroll on a sandbox

Before the first real cycle, run a sandbox payroll with sample data. Verify:

Basic + allowances calculate correctly
EOBI deduction shows on payslip
Provincial SS employer-side contribution shown
WHT calculated per slab
Net pay matches expected

Step 10: Run the first real payroll

Finalise attendance for the month
Verify approved leaves are reflected
Check overtime, advances, reimbursements
Generate draft payroll
Review draft per employee
Approve through workflow
Disburse via bank file
Distribute payslips

Step 11: File monthly statutory returns

EOBI monthly contribution + return (typically 7th of following month)
Provincial SS monthly contribution + return
FBR section 149 WHT deposit + monthly statement
Section 153 WHT for contractor payments (if any)

Step 12: Plan year-end

By end of fiscal year:

Annual salary tax certificate per employee
WWF return, if applicable (see the WWF guide)
EOBI annual return
Reconciliation: total WHT deducted vs deposited
Tax practitioner review

What founders usually get wrong

Starting with Excel ("we'll move to software later" rarely goes smoothly)
Delaying EOBI / PESSI registration
Wrong tax slab application
Not having a tax practitioner from day 1
No attendance setup ("we trust each other" works until it doesn't)
No payslips, which leaves employees feeling disrespected

The Zaffre HRM founder fit

Zaffre HRM comes with Pakistani statutory rules already set up. Most founders running their first payroll are configured and paying staff in under a week. Book a demo for a founder-focused walkthrough.

Caveat

Tax and compliance rules change. Always verify against current FBR / EOBI / provincial notifications and consult a tax practitioner. This article is general guidance, not legal or tax advice.

How to Run Payroll for the First Time in Pakistan: Founder Guide