The series was developed by Bernard Slade as a vehicle to keep Sally Field on the air after ABC's Gidget was cancelled, based on the 1965 book The Fifteenth Pelican by Tere Ríos.

Producer Harry Ackerman chose the deliberately eye-catching and easily marketable title 'The Flying Nun' instead of using the original book's title, 'The Fifteenth Pelican.'

Sally Field initially refused the role, finding the concept ridiculous while seeking more mature parts, but reconsidered after her stepfather Jock Mahoney warned she might not work again in show business if she turned it down.

Screen Gems' second choice for the lead, Ronne Troup, had already begun filming the pilot before being dismissed in favor of Sally Field.

Field recalled being humiliated on set, including one director who physically grabbed her shoulders and repositioned her like a prop, and she credited co-star Madeleine Sherwood for encouraging her to take acting classes afterward.

The San Juan convent courtyard exterior was actually filmed at Warner Brothers Ranch's backlot in Burbank, California, while only the pilot episode and the opening/closing credits were shot on location in Puerto Rico.

Because Sally Field was pregnant at the start of Season 3, props, scenery, and long shots of stunt doubles were used to conceal her pregnancy during flying sequences.

To ease concerns about how the Catholic Church would react to the show, the National Catholic Office for Radio and Television served as an on-screen credited adviser during production.

Screen Gems, following the model of The Donna Reed Show and The Monkees, had composers like Carole Bayer Sager and Dominic Frontiere contribute music, resulting in a 1967 Colgems LP of Sally Field singing songs from the series.