Synonyms for "little by little"
Solution 1:
There are quite a few —by— phrases at your disposal. The established ones, besides little by little are: step by step, day by day, inch by inch, and bit by bit. You can also construct any of your own choosing, depending on the context, e.g. moment by moment, sip by sip, limp by limp, and even wiggle by wiggle!
The plainest one-word synonym would be gradually. Other possible adverbs you could use in its place are: steadily, slowly, progressively and incrementally.†
I would also recommend the synonymous phrases, slowly but surely and by degrees.
†Credit goes to Martha for this suggestion.
Solution 2:
Perhaps 'gradually' may fit your needs, as it also suggests progression in small increments.
Solution 3:
You could also say
A little bit at a time