Yakshiyum Njanum starts with Minister Madhavan (Spadikam George) arriving along with his son Ranjith (Jubin) to consult astrologer Narayanji (Thilakan) regarding the bad omens that have been plaguing his estate. The minister is scared that these omens will cause an evil impact even on his ministership. The minister has several secrets to hide, the most prominent one among which is that he has provided shelter to a young man who is the chief accused in a murder case. Shyam, (Gautham) is a notorious goon for whom a man hunt has been launched by the local police. Meghna Raj plays the beautiful ghost in the film, who falls in love with Shyam.