Yes, you can withdraw the excess before taxes are due. "...

How late can I withdraw SEP overpayment for this year?

I did not make enough business income to contribute the maximum of $54,000. Can I withdraw the excess before taxes are due 4/17/18?

posted

Yes, you can withdraw the excess before taxes are due. "Employees who withdraw the excess contribution (plus earnings) before the due date for their federal return, including extensions, will avoid the 6% excise tax imposed on excess SEP contributions in an IRA."

Click the IRS link below for more information.

https://www.irs.gov/retirement-plans/retirement-plans-faqs-regarding-seps-contributions