On non-mortgage closed-end credit, the fee is usually withheld from the advance, and that is what makes the annual percentage rate exceed the note rate. Because a prepaid finance charge reduces the amount financed without reducing what is repaid, the borrower receives less than the face amount of the note while owing all of it, and the disclosed rate has to reflect that. Published material on personal loans works that arithmetic in full, including a worked comparison of a lower rate with a fee against a higher rate without one. Published material on debt consolidation loans covers the version of the problem that arises when the advance is supposed to pay off a known set of balances and arrives short by the fee. The point to carry into any comparison is that a rate and a fee are not separable questions, and the annual percentage rate is the figure that has already combined them.
On a mortgage the fee is usually paid at closing rather than deducted, and it sits inside a labeled block. The Loan Estimate groups the lender's own charges under "Origination Charges", which is where an origination fee, an application fee, an underwriting fee and any discount points appear. What a lender may and may not change between the estimate and the closing is governed by tolerance rules, and published material on closing costs covers those. The distinction worth carrying is between a charge that pays the lender and one that pays a third party, because the two behave differently both at closing and, as below, at tax time.
Federal student loans have a fee that is neither negotiable nor set by the lender. It is a statutory loan fee, deducted proportionally from each disbursement, and its percentage is re-set for each federal fiscal year by sequestration under the Budget Control Act rather than by any inflation adjustment. The Department of Education announces the applicable percentages for loans first disbursed on or after each October 1 in an electronic announcement to financial aid administrators. Because the figure changes on that annual cadence and applies by first-disbursement date rather than by academic year, the percentage for a specific loan is worth reading off the disclosure for that loan rather than off a general reference. The practical consequence is the same as on a personal loan: the school is credited less than the amount borrowed, and the borrower repays the full amount.
The tax question is the one that cuts across all three, and it turns on what the charge bought. IRS Publication 936 states that points "may also be called loan origination fees, maximum loan charges, loan discount, or discount points", so a line item labeled as an origination fee on a home loan may be points, and points are interest, deductible under the rules for points. In the same publication the IRS draws the other half of the line: "Amounts charged by the lender for specific services connected to the loan aren't interest", giving appraisal fees, Department of Veterans Affairs funding fees, mortgage insurance premiums, notary fees, and preparation costs for the mortgage note or deed of trust as examples, and stating that those cannot be deducted as points either in the year paid or over the life of the mortgage. The same test appears in the student loan rules, where Treasury Regulation section 1.221-1(f) treats origination fees that represent charges for the use or forbearance of money as interest; published material on the student loan interest deduction covers what that is worth. So an origination fee is deductible interest, or a non-deductible cost of getting the loan, depending on whether it was a charge for the money or a charge for work. The deductibility tests for points themselves, including the conditions for deducting in the year paid rather than over the life of the loan, are their own subject.
Two things a borrower can do with all of this. First, treat the fee as part of the price rather than as a separate question, and compare offers on the annual percentage rate rather than on the rate, because that is the figure that has already absorbed the fee on closed-end credit. Second, on a mortgage, read the Origination Charges block itemized rather than as a total, because the split between the lender's own charge and charges for specific third-party services is what determines both what can change before closing and what is treated as interest afterwards.