The guitarist has asked for the order against August Elizabeth Thomas to be granted from a Los Angeles court after she appeared uninvied at his house on July 28 and 29.
John said: "I feel like I'm being stalked," adding he feels he is "worried that she is unstable and that she could snap at any moment."
John - who left the Red Hot Chili Peppers in 2009 - explains how August initially approached him in 2010 proposing to write a screenplay about his life and hasn't left him alone since, sending a series of aggressive emails and letters, which he describes as "long, rambling and overly emotional - and in some cases, she would admit that she is 'often drunk.'"
August has also appeared at a number of shows by his musician wife Nicole Turley, to talk about the proposed screenplay.
The lawsuit, obtained by website TMZ, also states: "I fear both for my safety and for my wife's safety. Given that my wife and I are musicians and often play at venues around the world, it is hard for us to avoid Ms. Thomas if she is free to continually show up to harass us."
Both parties are due to appear in court later this month.