Jonathan Sims is the protagonist of The Magnus Archives. He shares a name with the series' creator, but is not intended as an author avatar or self-insert. He works as the head archivist of the Magnus Institute, an organization researching the supernatural, alongside coworkers Martin Blackwood, Tim Stoker, and Sasha James. He canonically enters a romantic relationship with Martin Blackwood in the series' final season. Over the course of the series, Jon becomes an avatar of an eldritch entity known as "The Eye", which grants him abilities of clairvoyance and pseudo-omniscience.

As his source material is audio-only, Jon has no canonical appearance, so accurate tagging may have to depend on word of the artist. He is often depicted as a slim or skinny brown-skinned humanoid with many eyes and scars.

In the source material Jon is asexual, but this is not necessarily the case in fan works.