The Liz & Dick actress is facing three misdemeanour charges from a June car crash and possible charges for an arrest on suspicion of assault in New York City.
Lohan has also allegedly had bank accounts seized by the IRS due to outstanding tax debts.
Littrell weighed in on the matter in a chat with TMZ, when asked if Lohan is in his nightly prayers.
"Unfortunately, no," the Backstreet Boy answered.
He continued: "I'm probably breaking a lot of ministers' hearts. It's like, 'He's a Christian. He should pray for everybody'. But she's not in my prayers at night. I'm sorry."
Lohan has received support from Demi Lovato and Mel Gibson, who recently said he might reach out to Lohan in the coming days.