Kyoto is widely regarded as the cultural capital of Japan, because of the numerous temples, shrines and palaces that are spread throughout - as well as encompass - the city. While not as ahead in the gluten free business as Tokyo, there are still some hot spots where you can find a bite to eat.
I have 2 pieces of advice for Kyoto:
1) always pack a lot of snacks. It's not uncommon to find yourself on the outskirts of the city at a shrine with no gluten free spots in site as most of them are in the city center. That, coupled with a lot of walking, can bring on some major hangryness.
2) If you are struggling to find gluten free food, try a vegan restaurant as they usually have better knowledge of food allergens and cross contamination.
Yak &Yeti is a Nepalese restaurant near the famous Nishiki Fish Markets in the Nakagyo Ward of Kyoto. Its a relatively big restaurant (by Japanese standards) with helpful and energetic server that speak English, and understand dietary requirements and happy to chop and change the meals to suit you. We chose the set menu for around 2000 yen each (£14) and we definitely weren't able to finish it all. Even if you were, they were happy to offer us free rice refills so we could finish the curries.
Lunch 11:30am-3pm. Dinner 5pm-10pm.
This restaurant is a very sweet multi storied place serving vegan food with gluten free options. I had a delicious green curry with corn chips and chocolate torte to finish. Salads and curries and mostly the choice for gluten free folk, but they also specialize in vegan burgers if you are travelling with someone who can have gluten.
Easily located of Shinkyogoku arcade, and next to some fantastic vintage clothing shops, it's definitely a place to pop to if your in the area.
Lunch 12-4pm. Dinner 6-9pm.
Other restaurants I am yet to try...
Kerala - An Indian restaurant with gluten free options in the city center.
Lunch 11:30am-2pm. Dinner 5pm-9pm.
Breizh Cafe - A creperie that sells gluten free buckwheat crepes
Premarché Gelateria Kyoto - An Ice cream shop with dairy free/vegan options with 2 branches in Kyoto
Open Thursday - Tuesday 12pm-6pm. Closed Wednesdays.
Kitten Company - A cosy vegan restaurant in the Shimogyo ward with gluten free options.
Open Monday-Friday 11am-7pm.
Kyoto Engine Ramen - A ramen restaurant in the Nakagyo ward with lots of gluten free options.
Open 11:30am-10pm Weekends, closed between 3:30pm-5pm on weekdays.
Sugarhill Kyoto - Japanese fusion restaurant with knowledgable staff. Booking recommended.
Open Monday-Saturday 5pm-10:30pm. Closed Sundays.