In the movie Serendipity, Sara asks Jonathan to write his name and phone number on a $5 bill, while she writes her name and number on the inside cover of a copy of Love in the Time of Cholera. If they are meant to be together, he will find the book and she will find the $5 bill, and they will find their way back to each other.
The book is referenced in How I Met Your Mother. It was Ted Mosby and Tracy McConnell's (aka the Mother's) favorite book.
The band Andrew Jackson Jihad reference the book in the title of their song "Love in the Time of Human Papillomavirus" on their album Can't Maintain.
In the TV show "Gossip Girl", While Nate is visiting Yale and pretending to be Dan, Jordan references this work when she says "What do you think about Marquez? Let's talk Cholera"
In the TV show "Agents of S.H.I.E.L.D.", season 2 episode 14 is titled "Love in the Time of Hydra".
The book is mentioned in the Jon Cusack film High Fidelity.