As of right now, nobody knows.
However when taking the timeline into consideration, she probably died in between the Third Great Ninja War and the Nine-tailed demon fox attack on Konoha by Tobi. It's more likely though that she died either in or soon after the Third Great Ninja War as Tobi states that his reasoning for not returning to the village was due to Kakashi being unable to save Rin and that by the time the Nine-tailed demon fox's attack occurs Tobi / Obito has gained an increase in ability and knowledge. This means that Rin must have died closer to the Third Great Ninja War otherwise Tobi / Obito would not possess the skill he does when fighting Minato / releasing the Kyuubi.