The story of Annayum Rasoolum is narrated by Ashley (Sunny Wayne) who works in the merchant navy and comes ashore in Kochi for the second time. On this trip, he recalls the events that happened when he was last here. He tells the story of Rasool (Fahadh Faasil), a Muslim tourist taxi driver from a modest background, who falls in love with Anna (Andrea Jeremiah), a Christian who is working as a salesgirl. Their love looks doomed to fail from the start.