Farrell married Etty Lau Farrell, a professional dancer who has performed in all the Jane's Addiction shows since the 1997 Relapse tour, in early 2002. The couple now have two sons together, Hezron Wolfgang and Izzadore Bravo.

In a video interview with Blender Online, Farrell says of his wife, "Etty and I have been working together since 1997. The very first time I saw her come in and shake her... ponytail, I hired her and I fell in love with her on the spot. We travel together and we have a collective memory. So in another words, I don't remember anything and she just reminds me of everything. So we share this memory bank. And it ain't a bad thing waking up with a hot chick in your bed everyday."