Billboard's Hot Christian Songs chart still has Lauren Daigle's 'You Say' at number one and Hillsong Worship at number one.
Lavigne, who became popular after her 2002 pop album Let Go, attended church in Canada when she was growing up but was never known as a 'Christian' musician.
Her latest single, the first in five years, is called 'Head Above Water' and contains the lyrics:
'God, keep my head above water
Don't let me drown, it gets harder
I'll meet you there at the altar
As I fall down to my knees'
It got 10,000 downloads in the first week since its release on 19th September.
Lavigne explained in a statement on her website that the meaning behind the song was to do with her struggle with Lyme disease, an infection spread by ticks which causes rashes and fatigue.
She says: "One night, I thought I was dying, and I had accepted that I was going to die.
"My mom laid with me in bed and held me. I felt like I was drowning.
"Under my breath, I prayed, 'God, please help to keep my head above the water.' In that moment, the song-writing of this album began."
"It was like I tapped into something. It was a very spiritual experience. Lyrics flooded through me from that point on."
She'd previously asked fans to keep her in their prayers on Twitter because of her health, as she saw various doctors across the country and said she barely made it through 2014.
"I went through a lot to get here", she concluded.
"The positive side is I didn't stop living my life. Having music while I was healing and in recovery definitely pulled me out of my darkness.
"I had a goal to work towards and a purpose. I hope the album touches people. We all go through challenges in life.
"Some, unfortunately, are more serious than others.
"Having gone through the battle of my lifetime, I'm stronger than ever and looking forward to sharing my renewed voice and energy for my life with my fans through this new music."
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