Others have given good advice. I'll risk being off base to give a different opinion. I'll assume she doesn't know you are agnostic, because she asked you to pray for her. Furthermore, you aren't ready to tell her because she is having a tough time. I would tell her that I would pray for her, and perhaps say a little (disingenuous) prayer to satisfy my anxiety about lying. That's a placebo to make her feel better.

Then, do the things everyone else said, which might actually help her.

Askher what you can do to help? Are you living near her? Is she ill? Figure out what you can do to help her. Financial? Child care? Cleaning? Cooking?

I tell people I will keep them in my heart's mind. That has to be as good as prayer, right?

I would lie and say I would pray for her,. Her comfort is more important than resisting her wish based on your disbelief.

Skirt the issue by asking if you can help in any way at the physical level.

If she knows you are agnostic or atheist, this is a form of emotional blackmail. I would offer what help I can but not succumb to praying.

I'd tell her yes then not do it.

Yes most time its a plea for help ..Not a reglious one.

Apparently she believes you are still religious? So I'd go with the flow and not cause more stress.

"I'm here for you if you need me"

I get that a lot I tell them my thoughts are with them. I know thoughts are as useless as prayers but it seems to make them feel better.

I'd tell her what she wants to hear, just to make her feel better, the do what you can by conventional means.

Similar things have been mentioned, but "I'll send good vibes" seems to work.

If it makes her feel good to hear you say you will, id tell her I will or have as she needed to hear.
That's not in anyway betraying your beliefs but comforting a friend.

How about if I take you to (lunch, shopping, a movie...)
How about if I cook a few things for you?
How about if I run a few errands for you?
Etc.
SO much more helpful than talking to the non-existent!

I have been in this situation before, and I usually just tell the person that I will. If it makes them feel better to think that I am praying for them, then so be it.

You are in my thoughts

tell her that you think about her all the time and that you are there fot her to talk to for emotionsl support.

Just make it what she want.. Not beacouse u belive or not.. just because she its impirtenant for you..!

While I don't believe in prayer per se, I do believe that sending positive thoughts cannot hurt.

I just say, "You'll be in my thoughts" instead of "I'm praying for you".

I would have lied and said I would.

The truth is that while there isn't proof that prayer works directly, there IS proof of the placebo effect, and just the comfort of thinking that someone might be trying to do some imaginary thought work could be enough to help her legitimately take a turn for the better, physically, emotionally, and otherwise.

In that spirit, DO offer that comfort, for her sake. What have you got to lose? A single breath, uttering words like "I'll keep you in my thoughts. I hope all this gets better, soon," might just work.

I say that I will keep them in my thoughts....

“You’re in my thoughts”