John II, lord of Chalon-Arlay (1312 – 25 February 1362) was a member of the House of Chalon-Arlay.

He succeeded his father Hugh I lord of Arlay to this title, and was himself succeeded by his son, Hugh II lord of Arlay.

Born in 1312, John was the son of Hugh I lord of Arlay and Béatrice de La Tour-du-Pin (1275–1347), the daughter of the comte Humbert I.

Before 1332, he married Marguerite of Mello (House of Mello,[1] daughter of the lord of Château-Chinon and of Sainte-Hermine Dreux IV of Mello, and of Eleanor of Savoy, daughter of the Duke of Aosta and Count of Savoy Amadeus V).

With Marguerite he had the following children: In 1361, he remarried to Marie of Geneva, daughter of Amadeus III, Count of Geneva.