Reading fanfiction for this pairing always requires a bit of a dig because it's less dominant than, say, Madoka/Homura, so you have to hunt with more care. The one story that consistently gets recommended is 'A Wind of Sharpened Glass.' It's an AU where they're both older and working in a sort of supernatural detective agency. The author nails Kyoko's defensive, sharp-tongued pragmatism and Sayaka's stubborn idealism, but it's the quiet moments where they're just sharing a bag of chips on a stakeout that really sell the slow-burn. The dialogue feels authentic to the show's vibe without being stiff.
For a completely different flavor, there's 'Sermons for the Fallen,' which is a post-Rebellion exploration. It gets extremely philosophical about grief, cycles, and what it means to heal when the world's rules have been rewritten. It's heavy, beautifully written, and the relationship develops through shared trauma rather than typical romance beats. Not a light read, but it stays with you.
If you want something with a bit more action and a supernatural twist that isn't just a rehash of the series, check out 'Red Strings and Blue Notes.' It's a crossover of sorts with another magical system, positioning them as rival magical girls from different factions forced to work together. The world-building is creative, and the tension between their opposing magical styles—Kyoko's more physical, Sayaka's more supportive—creates a fantastic dynamic for both conflict and eventual understanding.