Citi Bike is raking in millions of dollars in late fees — including from clueless tourists who don’t know the rules and annual members who constantly struggle to find a working dock, The Post has learned.

The bike-share program has collected more than $4 million in late fees since it started, with the bulk of the money coming from riders who get passes for a day or week.

Those riders — who can only use the bikes for 30 minutes at a time — have been hit with $2.9 million in fines as of the end of July. Annual members paid $1.39 million in penalties during that period.

Riders using short-term passes pay $4 if they go over 30 minutes, and $13 if they go over an hour. Every half-hour after that is a $12 fine. The fees are automatically charged to users’ credit cards, according to a spokeswoman.

Users with long-term memberships are billed $2.50 after 45 minutes and $9 after 75 minutes. It’s then $9 for every additional 30 minutes.

From when Citi Bike launched through July, riders were socked with the most fees in August of last year — over a half-million dollars in one month. Users were hit with the least amount this January, when snow blanketed the city. Only a little over $61,000 was charged to riders’ cards.

Katherine Kies, a 26-year-old from Chelsea, said she was hit with a $108 penalty after her bike didn’t dock properly.

“My account was shut down, and they didn’t give me any form of notification,” she said. “I fought it and they got rid of it, but I couldn’t use the bike that day. I was late.”

Chris Buttone, 43, a plumber who works in Manhattan, said he was hit with a late fee in June after his usual station on West 41st Street turned up broken.

“I had to find another station, and by the time I found one I ended up two minutes late,” he said. “And they charge you for that.”

A Citi Bike spokeswoman said riders can request a 15-minute time credit at a full kiosk so they can reach another station without paying extra money.

Real-estate agent Julien DuBois, 26, said the 45-minute window for annual users isn’t enough time to avoid a fee. “I’ve had a few, because sometimes it takes more than 45 minutes in the city,” he said. “It’s not a lot of time.”

The bike-share program, which has a six-year contract with the city, has had a rough financial ride in its first year and is reportedly millions of dollars in debt.

Additional reporting by Gillian Kleiman