In "The Kiss Seen Around the World", he is seen when a teacher, Mr. Lazenby is arrested for teaching that evolution was put into motion when Gil Gerard, star of the television series Buck Rogers in the 25th Century, “used a time machine, went back and ejaculated into the primordial ooze.”
He is mentioned in "When You Wish Upon a Weinstein" when Peter claims he is at Temple.
He was one of the townspeople who contributed to the mayoral debate between Lois and incumbent Mayor Adam West at the Quahog Community Center in "It Takes a Village Idiot, and I Married One", asking Lois what she plans to do about crime in a rare out-of-school appearance.
He also appears in "Stew-Roids" at Chris's downfall.
Chris gets in trouble for telling a dirty joke in "The Splendid Source", so Shepherd has a meeting with his parents regarding the incident.
He is arranged and held the assembly for Chris's essay contest victory in "New Kidney in Town".
Principal Shephard calls a conference with Peter and Lois when Chris does poorly in school in "Space Cadet".
During the nominations for class president in "Secondhand Spoke", Principal Shepherd notes to himself that there is no one that looks hot that year among the students.
In the courtroom scene in "The Simpsons Guy", he is seated next to the similarly dressed Principal Skinner.
Principal Shepherd gets buff with new workout equipment, which he claims isn't due to his divorce in "Once Bitten".
Principal Shepherd, who is given the first name of "John" in "Crimes and Meg's Demeanor", has another spat with his ex-wife Fiona. Brian, who has taken up spying on the neighbors in the apartment across the street from his observes this and his dragging of a large garbage bag out that leaves a trail of red liquid behind and a report of her missing comes in later still. He tries to call in his concerns to Joe who can't help him without more solid evidence. He calls Stewie who tries to help him by checking Shepherd's apartment when he steps away. Stewie is nearly caught once but disguises himself as one of Shepherd's dolls. After receiving some unwanted attention, Stewie tries to escape and is spotted, with Principal Shepherd spying back at Brian's apartment. He confronts Brian and Stewie who smacks him with a paddle which results in Brian being knocked out of a window. With the medic and police present, they find Shepherd's bag and find it is full of food taken from the school due to his ex-wife's departure and has been safe during this time.
- FG214 "Let's Go to the Hop"
- FG308 "The Kiss Seen Around the World"
- FG310 "A Fish out of Water"
- FG322 "When You Wish Upon a Weinstein" (mentioned)
- FG505 "Prick Up Your Ears"
- FG516 "No Chris Left Behind"
- FG517 "It Takes a Village Idiot, and I Married One"
- FG713 "Stew-Roids"
- FG819 "The Splendid Source"
- FG908 "New Kidney in Town"
- FG913 "Trading Places"
- FG917 "Foreign Affairs"
- FG1021 "Tea Peter"
- FG1109 "Space Cadet"
- FG1204 "A Fistful of Meg" (heard only)
- FG1206 "Life of Brian"
- FG1215 "Secondhand Spoke"
- FG1219 "Meg Stinks!"
- FG1301 "The Simpsons Guy"
- FG1307 "Stewie, Chris & Brian's Excellent Adventure"
- FG1308 "Our Idiot Brian"
- FG1315 "Once Bitten"
- FG1316 "Roasted Guy"
- FG1413 "An App a Day"
- FG1416 "The Heartbreak Dog"
- FG1419 "Run, Chris, Run"
- FG1502 "Bookie of the Year"
- FG1505 "Chris Has Got a Date, Date, Date, Date, Date"
- FG1513 "The Finer Strings"
- FG1518 "The Peter Principal"
- FG1605 "Three Directors"
- FG1608 "Crimes and Meg's Demeanor"
- FG1706 "Stand By Meg"
- FG1713 "Trans-Fat"
- FG1715 "No Giggity, No Doubt"
- FG1719 "Girl, Internetted"
- FG1720 "Adam West High"
- FG1805 "Cat Fight"
- FG1807 "Heart Burn"
- FG1809 "Christmas is Coming"
- FG1810 "Connie's Celica"