SEP IRAs are subject to the same withdrawal rules as Traditional IRAs. SEP IRA contributions and earnings may be withdrawn at any time, but there are penalties that may apply, using the same rules as those applied to Traditional IRA withdrawals.

If you are under the age of 59½, you must pay a 10% penalty fee in addition to income taxes on your withdrawal. Of course, there are certain exceptions to the penalties: first time home-buyers expenses up to $10,000, medical bills, educational expenses, and a few others.

If you are over age 59½, you will only have to pay income taxes on the amount you withdraw. Once you reach age 70 ½, you are required to begin taking Required Minimum Distributions, according to IRS guidelines.