This article includes the detailed steps for setting up the ClockOn Online system based on details already available from the ClockOn desktop version.

Included in this article are details on how to;

  1. Register A ClockOn Online Account
  2. Replicate The Basic Items For Your Existing Setup
  3. Enter The Employees
  4. Finalise The ClockOn Desktop Setup
  5. Confirm The Payroll Period Ranges
  6. Migrate Employee Leave Balances (Optional)
  7. Migrate Employee YTD Balances (Optional)

Please be aware that this process will not migrate your existing payroll information, you will still need to be maintain your desktop version records separately for the appropiate amount of time.

Register A ClockOn Online Account

To get started with ClockOn Online you will need to create and sign into your online account at

If you do not currently have an account you can create one using the Sign Up link as shown below. 

During this process, you will be asked for your email address, and create a password. At this step, you will also need to enter your company's details such as address and ABN.  

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Replicate The Basic Items For Your Existing Setup

Once you have your login for your account, and the company has been registered, the next step is to establish a baseline setup relevant to your business. 

The items that we recommend checking include the following;

  1. Rule Sets
  2. Locations & Departments
  3. Roles (Optional)
  4. Payslip Categories (Optional)
  5. Allowance Sets (Optional)
  6. Rate Sets (Optional)

Rule Sets

The rulesets are used to set the conditions that the employees will be paid under within the payroll process. They are designed to house important details such as; employment type, overtime and penalty conditions, leave accrual rates, and super settings. 

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The rule set screen can be accessed on the ClockOn Online version from the Setup > Rule Sets menu item.

On the creation of a new ClockOn Online account the system will automatically create 4 generic rulesets

  1. Casual
  2. Full Time
  3. Part Time
  4. Salary - Full Time - 38hr week

If your rule sets are needed beyond the provided presets, they can be modified, or additional configurations can be added. 

The Rule Sets Overview article details the process for adding new rulesets as well as the options available within them.

USEFUL TIP: As the listing of rulesets can be extensive, it may be useful to identify which instances are currently in use so to reduce the amount of manual work required to migrate to the new setup. 

This can be done by using a report from the Desktop version, such as the "Employee Listing (rule set, allowance / deduction set, rate set)".

For your reference you can open and view the rule sets details on the desktop version by using the steps below.

Locations & Departments

Locations and departments are important components of the ClockOn system. They are used for everything from sorting the employees to employee payroll costing allocations. 

On the creation of a new ClockOn Online account, the system will auto-create a location and add a linked department named "Default" for the location to allow for quick usage of the system. 

This is a basic starting point, and for customers wanting to use advanced payroll department costings, we recommend a review of these settings.

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To view and update the settings in ClockOn Online use the Setup > Locations menu option.

Edit the location or department using the Options button from the locations line.

You can find information on the available settings for this section in our Locations and Departments article.

For your reference, you can find the existing location and department settings on the Desktop version. 

For a detailed overview on the settings available within this section, please see the Location Manager guide

Roles (Optional)

Roles allow you to segment your employees by the functions that they perform within the business within their departments and are generally used when rostering team members. Qualification records can also be linked to roles which can further enhance the rostering to allow the roster officer to ensure that the employees are qualified for the role that they are being assigned.

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To access the setup for the Roles, navigate to it using the Setup > Locations menu item.


Then select Roles from the location's Options button 

The settings from the ClockOn desktop version can be found under Locations > Roles

The settings for this are added to the ClockOn Online system from the Locations screen

For more details on how to setup and use roles refer to the Roles & Qualifications article.

Payslip Categories (Optional)

Another feature is to add payslip categories, these allow you to indicate the employee's job description on the pay slips. The following guide details how you can locate these settings on the Desktop version. Payslip Categories.

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To add these to the ClockOn Online, open the Setup > Additional Settings screen 

Then select Payslip Categories

For your reference below are the steps to locate the payslip category settings on the desktop version of ClockOn.

Allowance Sets (Optional)

Allowance Sets are used to allocate a preset listing of generic allowance items to the employees on-mass rather than needing to add them against the employees individually. This also allows for quick updates to these allowances across all linked employees if the condition for the allowance changes, for example, the rate needs to be adjusted.

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The following details how you can add an allowance set into the system.

The allowance set detail can be located on the desktop version  

Rate Sets (Optional)

Rate sets are a useful tool for employees paid based on an award wage. If set, and linked to the employees they will prompt the payroll officer to update the employee's hourly rate if it is lower than the indicated award wage. 

They can be set to trigger on any one of the following

  1. Based on changes in the age of the employee, 
  2. When they meet an industry hours criteria, 
  3. Based on the number of years worked with the business.

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Within ClockOn Online, the rate set settings can be found under the Setup > Rate Sets menu option.

For details on how these can be set up within the ClockOn Online system please see the Rate Sets article.

If these have been established in the desktop version, the settings can be located using the Setup > Rate Schedules menu option.

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Adding Employees

Once the base setup is complete you are now ready to begin to add the employees into the ClockOn online system. 

Employees can be entered into the ClockOn Online system in 3 ways

  1. Manually
  2. Using Employee Onboarding (via the FLARE integration)
  3. Using the Employee Import process 

For the details on this process, please refer to the Adding Employees article.

For customers with a large number of employees, the ClockOn Online system has the facility for an employee import process. This allows for on-mass import and update of employee details into the system, the following article details the process for this as well as a specification for the file fields that can be imported Employee Import.

Our team can provide an export file for the ClockOn Desktop system to assist with this process. If you are interested in this service, please contact our team at

The existing ClockOn Desktop employee information can be found through the Setup > Employee Details menu option.

Please see below to answer a frequently asked question that is asked is how to setup allowances against employees.
The article Payroll Adjustments (Allowances & Deductions) - Examples provides details on some common configurations. 

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Finalise STP For Employees In ClockOn Desktop

Once you are happy with the initial setup and you have done your last payroll in the ClockOn Desktop system, the next step is to run a final process to close off your STP submissions for the financial year on the ClockOn Desktop system. 

IMPORTANT: If this step is not completed, the employee's MyGov records will not be marked as Tax Ready for current financial year.

To finalise the employee information use the steps below

  1. Open the Single Touch Payroll wizard, 
  2. select the Employee Update 
  3. Ensure that the correct ABN and Year Ending is chosen 
  4. Check the Final Payroll Indicator option
  5. Proceed through the wizard 

For a detailed guide on this process please see our Single Touch Payroll (STP) - EOFY Submission article.

USEFUL TIP: With the STP system there is no need to re-run the payrolls that you have done in a previous system. You can simply pick up where you left off within ClockOn Online.

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Confirm The Payroll Period Ranges

During the initial setup for ClockOn Online, you would have been prompted to indicate your upcoming payroll period cycle. It is a good idea to double-check that these settings are still correct as additional payrolls may have been done since through the Desktop version.

The following details how this can be checked on the ClockOn Online system.


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Migrate Employee Leave Balances (Optional)

If you are tracking your leave employee's leave balances through ClockOn then you will need to manually migrate the balances from the ClockOn Desktop system through to the ClockOn Online system.

The following guide details how to locate the individual leave settings for the employees in the ClockOn Online system.

You can locate the employee's current leave balances on the Desktop version using the guide below.

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Migrate Employee YTD Balances (Optional)

As an optional step, you may want to add the employee's year-to-date balances from the ClockOn Desktop system to the ClockOn Online system. The benefit of doing this step is that it gives your employees visibility on the total year-to-date earnings for the financial year when they retrieve their payslips.

PLEASE NOTE: This step is entirly optional, the ATO will already have the amounts processed though the desktop version that the employee can view on their MyGov portals. 

The following guide details how you can enter the employee's YTD balances into the ClockOn Online system.

NOTE: As this is generally only used for showing the total gross and tax amounts on the employee's payslips, you can usually shortcut this to just updating these amounts, rather than matching it to what would be needed to submit to STP. 

The following guide details how you can view the employee's current YTD balances on the desktop version.

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