Charlie attended Oberlin College's Galactic Safe Sex Ball party as a sophomore, where he was introduced to Marnie by Elijah. Marnie had had a bad reaction to marijuana brownies, and Charlie comforted her. After the party, they started dating.
Charlie's best friend, Ray Ploshansky, performs with him in their two-man indie band, Questionable Goods.
Charlie and Marnie have been together for four years by the Pilot, and he is perfectly happy in the relationship. But the passion has long since died out for Marnie, who wishes her boyfriend could be less obsessed with her emotions and a little more dominant.
In Vagina Panic, Charlie and Marnie have sex. Shortly after, they argue about how she's not actually physically attracted to him.
He surprises Marnie with his newly shaved head in All Adventurous Women Do, which she finds repulsive until he explains he did it in support of a co-worker who is battling cervical cancer.
In Hannah's Diary, Ray finds Hannah's journal while he and Charlie are assembling a coffee table in her apartment. During a Questionable Goods gig, Charlie reads Hannah's journal entries stating Marnie's true feelings for him. Marnie is humiliated as Charlie goes off on a tirade that makes her seem like a cold bitch.
Charlie breaks up with Marnie in the following episode, despite her claims that she actually loves him. Yet he takes her back after she goes to his apartment and promises to not take him for granted. Almost immediately after having awkward and underwhelming make-up sex, Marnie agrees they need to end their relationship.
Two weeks later, Marnie attempts to talk to Charlie at a rave in Welcome to Bushwick a.k.a. The Crackcident. She backtracks when she sees he has a new girlfriend named Audrey. Marnie is stunned that Charlie already has a new girlfriend and isn't pining over her.
They run into each other at Jessa's surprise wedding in "She Did" and appear to be on friendlier terms. It's hinted that Charlie still harbors feelings for Marnie when he jealously watches her flirt with another guy.
Charlie and Audrey are still together, and they attend Hannah and Elijah's party in It's About Time. Later, he receives a visit from an upset Marnie and lets her stay the night.
Charlie brings Audrey to a dinner party thrown by Hannah in It's a Shame About Ray, and Audrey breaks up with Charlie when she realizes he still loves Marnie. Charlie follows Marnie to the roof and tries to make a move on her, but she rejects him. Hannah yells at him when he tries to blame Marnie for causing their break up.Marnie visits Charlie in It's Back after hearing that he created a successful app and runs the startup out of his own office. His inspiration for the app also comes from Marnie - it blocks you from contacting your ex. After she embarrasses him at a company party in On All Fours, they fight and have sex in his office.
By the episode Together, they're still hooking up. Marnie is angry with Charlie about the unclear direction of their relationship; she doesn't know what he wants from her. She admits she still loves him and he says he wants to be with her again, so they get back together. The two are last seen smiling and walking together in Manhattan.
In the season premiere, Females Only, Charlie and Marnie broke up again after living together for several months. Adam mentions that he ran into Charlie recently. In She Said OK, we see Charlie posted an embarrassing music video of Marnie doing Edie Brickell’s “What I Am” on YouTube.
The story behind Charlie and Marnie's second break up isn't revealed until Beach House, in which Marnie explains that Charlie called her and claimed he wanted to propose, but that they needed to talk in person first. Charlie then came home and began packing his things. He told Marnie that he didn't love her and he never had. He left and never contacted her again.
Marnie also mentions that Charlie's app startup tanked and he has since become a carpenter's apprentice.
Charlie re-appears in The Panic in Central Park when Marnie runs into him on the street. Charlie looks completely different, with an affected accent, a beard, and tattoos.
Marnie is totally taken aback by his cool confidence and newfound masculinity. Ironically, she now finds his shaved head attractive - he's no longer the sensitive, overly attached guy who drove her crazy with his smothering ways.
Charlie comes clean to Marnie that he had abandoned her and his old life because his father committed suicide. At the time, he had no idea how to handle it.
He takes Marnie to an upscale party and she discovers that he has become a drug dealer. Initially, Marnie is accepting of Charlie's risky new lifestyle and they head back to his dingy apartment. After they sleep together, he asks Marnie to run away with him and she accepts. But after she finds heroin and syringes in Charlie's jeans, Marnie leaves without saying goodbye.