I have a cousin whom I love dearly. She is going through a tough time and has asked me to pray for her. I want to help, but I don't believe in prayer. What would your response have been?
I guess I would have done the same thing, it all depends how bad off she was, if she was dying I would have given in cause if I loved her , and she on her way out and it would have made her feel better ,so what. But if she was just wineing and complaining a bout her boreing ass then I would given her the hard love and told her just what I thought, its all about being part of the solution and not part of the problem, but that's a tough one?
Just say ok... you wish her well, that’s the same thing and has the same outcome, so just say ok... And then just to lighten up the mood perhaps say something like, “how about that Darwin?”
I will not lie and say I'll pray, but that's me. I tell people I'll send good thoughts their way and keep them in mind. I think they are looking for some type of comfort and help, give her a hug and tell her she is always on your mind.
Just my two cents, for what it's worth.
Do things instead, give her a ride, help in whatever way you can, just be there . . .
Actions speak louder than prayers
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 just say, "You'll be in my thoughts" instead of "I'm praying for you".
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.