Short answer
Yes, in one of two ways. You can pay off the HELOC as part of the refinance, or the HELOC lender can agree to subordinate, meaning it stays in second place behind your new first mortgage. Subordination needs the HELOC lender's approval and can take a few weeks. Paying off a HELOC that wasn't used to buy the home usually makes the refinance a cash-out refinance under Fannie Mae's rules, which can change the pricing and limits.
Why does the HELOC matter when I refinance?
Liens generally rank in the order they're recorded. Your current first mortgage is in first place and the HELOC is in second. When the refinance pays off the first mortgage, the HELOC would move up to first place unless its lender agrees in writing to stay behind the new loan. Your new lender requires first place, so the HELOC has to be paid off or subordinated.
How does subordination work?
Your loan officer or title company sends the HELOC lender a request with the new loan's details. The HELOC lender reviews it, sometimes with its own appraisal or fee, and signs a subordination agreement that's recorded with the new mortgage. Each lender has its own rules and turnaround time, so start early and ask about it before you lock your rate. See how rate locks work.
What if I pay off the HELOC in the refinance?
Under Fannie Mae's rules for a limited cash-out (rate and term) refinance, only a second lien that was used to buy the home can be paid off and rolled into the new loan, with a narrow exception for energy improvements. If you used the HELOC for renovations, debts or anything else, paying it off generally makes it a cash-out refinance. See cash-out refinancing in NH.
Which option is better?
Keeping the HELOC can preserve a lower rate on it or keep the line open for future use. Paying it off simplifies things into one payment, but it may cost more as a cash-out refinance. Tom can price both ways and show the difference. See HELOC vs. cash-out refinance and when to refinance.
Sources
Checked November 2, 2026. Rules and dates change, so confirm current details before you rely on them.
General information only, not tax or legal advice. Program availability, eligibility and terms vary by lender and are subject to change and to underwriting approval. Not a commitment to lend.