IHOP Corp. said last week that it has settled a dispute with the Internal Revenue Service over its federal income taxes spanning 2000 to 2003, agreeing to pay $11 million in taxes and interest.

The dispute was related to the tax treatment of certain franchise fees the Glendale-based restaurant chain owner received. The company said it agreed to pay the fee, which includes $7.7 million in federal income taxes and $3.3 million in interest with no penalties due.

In the agreement, IHOP will report additional income for those tax years which will increase its federal income tax liability. It will also amend its 2004 and 2005 federal tax returns to reflect the agreement, which is expected to result in a $3.1 million refund in previously paid federal income taxes.

IHOP also said the settlement is not expected to affect the company’s past income statements or future accounting practices.

Shares in IHOP were up 4 cents to $53.97 in early trading Monday.