Musee des Beaux-Arts de LyonFine arts museum on Place des Terreaux, in a former abbey with a quiet cloister garden that works as a break. Free under 18. Guided visits for families and kids from 18m+. Ask for the free activity books for your little ones at the reception (in FR).
Musee des ConfluencesScience and anthropology museum in a striking building where the rivers meet, covering natural history, societies and the origins of life. Lifts throughout and plenty of space for a buggy. Free under 18. Lots of workshops for all ages in French.
Musee GadagneTwo museums in a Renaissance mansion in Vieux Lyon: the history of the city, and a puppet museum built around Guignol. Both are free under 18.
Musee Miniature et CinemaTwo collections in one building in Vieux Lyon: miniature scenes built at tiny scale, and props and effects from film sets. Around an hour and a half. Free under 4.