The Phanatic replaced "Philadelphia Phil" and "Philadelphia Phillis", a pair of siblings dressed in 18th-century garb to invoke the city's revolutionary spirit from 1776. The pair were in the team logo from 1976 through 1978, and were part of the team's "Home Run Spectacular" at The Vet from 1971 through 1979. They reappeared with their replacement as the Phillies celebrated their final year at Veterans Stadium in 2003, including opening day and the final game.

During the winter after the 1977 season, Dennis Lehman, who along with the Philadelphia Phillies Promotions Director, Frank Sullivan, thought the team needed a mascot similar to the Padres' San Diego Chicken, created the Phanatic with help from Harrison/Erickson of New York City (now known as Acme Mascots), which had ties with Jim Henson's Muppets. Instead of a number on the back of his jersey, he wears a star. The character was named for the fanatical fans of the team.

The Phanatic was originally portrayed by David Raymond, who was then working as an intern in the team's front office, for fifteen years, from 1978 to 1993. Raymond's father is retired Delaware Blue Hens Hall of Fame coach Tubby Raymond. Since 1993, Tom Burgoyne has portrayed the Phanatic, although in public - in order to retain the illusion that the Phanatic is a real creature - Burgoyne maintains that he is only the Phanatic's "best friend."

There is a running gag where the Phanatic humorously mocks opposition players and they would steal his ATV keys in retaliation. However, the Phanatic's antics are not always popular with opposition players and coaches. The Dodgers' Tommy Lasorda in particular did not like the Phanatic's mocking of the Dodgers. In 1988, he assaulted the Phillie Phanatic during a nationally televised game after the Phanatic stomped on a life-sized dummy wearing Lasorda's uniform (reportedly provided by Dodger infielder Steve Sax).

In 1989, Orlando's NBA expansion team, the Magic, was founded largely through the efforts of former Philadelphia 76ers General Manager Pat Williams. Williams introduced Stuff, a furry green dragon with similarities to the Phillie Phanatic, as the team's official mascot. When Williams staged the "birth" of Stuff at an Orlando event, the man inside the Stuff was Dave Raymond.

The Phanatic's head disappeared during the Phillies' "Final Pieces" charity sale and auction in 2004. Tom Burgoyne had taken off the costume for a break and found the head missing when he returned. One week later, someone anonymously called a local radio station claiming that he found the head and would bring it to the radio station. Police arrested and charged Bernard Bechtel with felony theft after he brought the $3,000 head to the station.

In 2005, David Raymond founded the Mascot Hall of Fame, and the Phanatic was inducted as a charter member. Since 2003, Burgoyne has written several children's books, published by the team, featuring the Phanatic.

The Phanatic appeared in the closing credits of the film Rocky Balboa (2006).

The Phanatic was voted "best mascot ever" by Sports Illustrated Kids. In January 2008, Forbes magazine named the Phanatic the best mascot in Sports.

In 2009, the Phanatic was one of several recipients of the Great Friend to Kids (GFTK) Awards, given by the Please Touch Museum (the Children's Museum of Philadelphia).

In 2010, an assortment of 5 feet (1.5 m) tall, 100 pounds (45 kg) fiberglass statues were painted by artists and placed on display throughout Philadelphia from April through August with all monies raised going to Phillies' Charities.

On January 26, 2012, the Phanatic (credited to Tom Burgoyne) appeared as itself on an episode of the NBC sitcom 30 Rock called "The Ballad of Kenneth Parcell".

He and Mr. Met did a MasterCard commercial in 2013 to raise money for ending cancer.

The Phanatic was also on an episode of the show The Goldbergs in 2014 called "The Lost Boy", and made a cameo appearance on College GameDay when the ESPN show visited Philadelphia for a matchup between Temple and Notre Dame.

In 2015, Good Morning America bestowed the honor of the best mascot in baseball on the Phanatic.