Although more commonly know by the first half, the full title of Mary Shelley's novel is: Frankenstein or The Modern Prometheus. Both parts of this title refer to the main character, Victor Frankenstein. It is important to note that his creation, the monster, is unnamed.
In order to understand the comparison being made in the title, we need to look at Prometheus in Greek mythology. Prometheus was one of the Titans, who existed before the Greek Pantheon of gods. He is given credit for creating human beings from clay, water, and divine breath. In trying to advocate for humans, Prometheus inadvertently angers Zeus who punishes humanity with misery and illness. Finally Prometheus is sentenced to an eternity of torture for bringing fire (which represents enlightenment and knowledge) to his creatures.
From this description, there is a clear comparision between Prometheus and Victor Frankenstein. Both sucessfully created human life and faced results not in line with their expectations. In an attempt to help their creations, both Prometheus and Victor Frankenstein caused more damage and disorder. This eventually led to the harm of both, either through death or eternal torture.