For many doctors, end of financial year is treated as an administrative deadline.
Tax return. Super. Deductions. Maybe a quick conversation with the accountant.
But for doctors earning through an ABN, working through a company, or managing a mix of locum and permanent income, EOFY is much more than that. It is the one point in the year where several financial decisions converge at once.
Get them right, and you start the new financial year with better clarity, stronger cashflow, and fewer surprises.
Get them wrong, and you can spend the next 12 months or longer correcting issues that could have been prevented before June 30.
This is not a generic EOFY checklist. It is a decision guide.
Because the right answer depends on your situation. An IMG in their first Australian financial year faces different issues from a GP contractor, and both are different again from a practice owner preparing for growth or a future buy-in.
These are the four decisions worth reviewing before June 30. Generally, the earlier it's done the better the outcome will be.
If you are paid through PAYG employment, tax is generally withheld for you as you go. Super is also paid separately, and your year-end position is often relatively straightforward.
If you are earning through an ABN or company, it is a different story.
The income arrives gross. Nothing is automatically withheld. The tax obligation builds quietly in the background, and many doctors do not feel the full impact until their return is lodged.
For first-year contractors, this can be even more painful because the first large tax bill is often followed by PAYG instalments for the next year. In practical terms, that can mean paying last year’s tax while also being asked to start prepaying the next year’s.
A simple rule of thumb is to set aside at least 35 percent of each payment into a separate account that is not used for day-to-day spending. If that has not happened consistently this year, it is better to calculate the shortfall now than discover it later when the tax bill arrives.
IMGs in their first year in Australia
You may have worked across a mix of PAYG and ABN roles, often without a clear sense of how the overall tax position will land. That is worth
calculating before June 30, not after.
GP contractors
A structure change mid-year can complicate things. Moving from sole trader to company, or changing the entity through which you are paid,
can leave income split across multiple arrangements.
Practice owners
Your personal tax position and your practice entity’s obligations are separate issues. If multiple entities and trust distributions are
involved, it can get quite complex. Timing and documentation around year end become particularly important.
Super contributions are often discussed as a last-minute EOFY strategy, but for doctors, the real question is usually more specific than that.
It is not just whether to contribute.
It is whether a contribution makes sense this year, how much room remains under the concessional cap, and which entity should be making the contribution.
For the 2025–26 financial year, the concessional contributions cap is $30,000. That includes employer super guarantee contributions. So if you are on PAYG income, part of that cap may already be used before you make any personal contribution yourself.
If you operate through a company, the contribution pathway may be different again. If you are a sole trader, personal deductible contributions may be the relevant mechanism.
This is where many doctors run into problems. A contribution can reduce taxable income, but it still affects cashflow. If making a contribution leaves you short for an upcoming tax payment, loan commitment, or PAYG instalment, the decision may not be helping as much as it appears.
There can also be opportunity here.
Doctors who were on lower registrar incomes in prior years, and who did not fully use their concessional caps, may have unused amounts available to carry forward. This often becomes relevant after fellowship, when income rises materially and the value of contribution planning changes.
This is the decision many doctors postpone, especially if the current setup is “working well enough.”
But EOFY is often the most sensible time to review whether your structure still fits the reality of the year ahead.
A structure that made sense 12 months ago may not be the right one now if:
The cost of staying in the wrong structure is not always dramatic in a single month. It compounds over time through unnecessary tax, weaker cashflow, reduced lending capacity, extra admin, and the cost of maintaining entities that no longer serve a clear purpose.
You set up a company this year to satisfy agency requirements
It is worth reviewing whether that company is only acting as a payment vehicle, or whether it should also be handling super, deductions, and
broader planning properly.
You are thinking about buying into a practice in the next 12 to 24 months
The structure you use now may affect how cleanly that acquisition can happen later. It is usually easier and cheaper to address structural
issues before the buy-in than after it.
Your income increased significantly this year
Crossing key thresholds can change what is optimal. That may include marginal tax rates, Division 293 exposure, Medicare Levy Surcharge
implications, and broader structuring considerations.
This is the most familiar EOFY issue, but it is still where many doctors lose money or create unnecessary risk.
For locum and contractor doctors especially, deductions can be more varied than for salaried employees. Depending on how the income is earned, relevant expenses may include professional indemnity insurance, equipment, professional development, home office costs, and travel between work locations.
The issue is not just what might be deductible.
It is whether the records are complete, whether the claims are supportable, and whether the treatment matches the way the income was earned.
For doctors with investment properties, one of the most commonly missed deductions is the interest deduction on their deposit amount. The tax benefits foregone can be in the thousands. The key is having the loan structured correctly at the start and the interest amount tracked separately.
Good deduction management is rarely about scrambling in July. It usually comes from keeping clear records throughout the year, so claims can be made confidently and supported if ever questioned.
If you are not confident that your deductions are complete, or if you are unsure whether what you are claiming is actually defensible, that is critical to have it reviewed before June 30, not after.
On paper, these decisions can look separate.
In practice, they interact.
A super contribution affects cashflow.
Your structure affects which deductions are available and how income is reported.
Your tax position can affect borrowing capacity.
A decision that helps in one area can create pressure in another.
That is why many doctors do not get the full benefit of EOFY planning from a generic checklist.
The doctors who tend to navigate EOFY well are not the ones trying to tick every box. They are the ones who review the bigger picture early enough to make decisions while options still exist.
Before June 30, the goal is not just to “do your tax properly.”
It is to make sure your tax position, structure, cashflow, and future plans are actually aligned for the next financial year and with your long term financial priorities.
For doctors with mixed income, contractor arrangements, entity changes, or upcoming practice decisions, that review can be far more valuable than another last-minute EOFY tip list.
Not sure where things currently stand?
The Doctor Financial Scorecard is designed to help doctors get a clearer view
of their tax, structure, cashflow, and lending readiness before the new financial year begins. Feel free to reach out if you need specialist guidance with your specific financial decisions.
Tommy Li, CA
Director, Verity Advisory | Registered Tax Agent | Authorised Financial Adviser (ASIC Rep No. 1261831) | Member, Chartered Accountants Australia & New Zealand
Tommy is a Chartered Accountant with 20+ years advising medical professionals on tax, financial structure and practice decisions. He founded Verity Advisory to provide integrated advice for doctors at career-defining financial inflection points — combining tax, lending and financial planning into a single structured approach.
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