Pep Comics introduced the superhero character The Shield, the first of the super-patriotic heroes with a costume based on a national flag (predating Captain America by over a year), as well as The Comet.

The format of Pep Comics was very similar to the previous titles; 64 pages of short strips, initially featuring a mixture of science-fiction stories such as "The Queen of Diamonds" (#1–12) by Lin Streeter (renamed "The Rocket and the Queen of Diamonds" in #2 (Feb. 1940)), about a John Carter of Mars-like hero trapped on another planet; the crime fighting story "The Press Guardian" (#1–11) by Jack Binder and Mort Meskin and later Abner Sundell and Meskin (retitled "Perry Chase, The Press Guardian" from #7);[2][3] and three adventure tales, "Sergeant Boyle" by George Biro, about a soldier fighting with the British in Europe, as the United States was not yet involved in World War II,[4] "The Midshipman", (#1–16) "Lee Sampson, Midshipman" from #6 (July 1940), following Lee Sampson through Navy College to his Graduation,[5] and an adventure based on boxing, "Kayo Ward" (#1–28) by Phil Sturm.

The last was similar to "The St Louis Kid" in Top-Notch Comics, both characters progressing through the boxing championships hierarchy throughout their series.

Two short humor strips also featured in the first issue, "Jocko" and "Animal Antics", both by Dick Ryan, while "Buttonhead" by Quincy appeared in #2–5.

The Shield and later The Hangman and Black Hood also featured in single page text stories during the MLJ years of the title; all comic books did this through the early 1960s to satisfy United States Postal Service requirements for magazine rates.

Written by Joe Blair, with art by Jim Streeter, Fu Chang is a "Chinese scholar and detective, heir to the magic secrets of Aladdin who uses them only to bring peace and good-will to the people of his Chinatown.

Another featured character was "Bentley of Scotland Yard", a mystery detective story originally by artist Sam Cooper and later Paul Reinman.

Each story was in a horror/fantasy vein, with Bentley up against creatures such as a werewolf in #1, a monster in a lake in #2, and hunchbacks, devils and vampires through the first 41 issues of Pep Comics.

With issue #11 (Jan. 1941), "Fu Chang, International Detective", "Perry Chase, The Press Guardian" and "The Rocket and the Queen of Diamonds" ended.

"Danny in Wonderland", a surreal fairy-tale adventure by Harry Shorten and Lin Streeter with stories loosely based on fairy tales such as "Cinderella", "Pinocchio", and The "Little Mermaid" (#12–39), while Ted Tyler, "The Fireball" (#12–20), 'sworn enemy of all who use fire for evil purposes' [10] was a fireman who gained flame powers from a mixture of chemicals while fighting an arson attack.

Madam Satan, a dead villainess with a green face and the kiss of death, "the scourge of man, ready to go forth and leave a trail of misery and suffering in her wake" actually first appeared on the cover of the previous issue #15 (May 1941).

Madam Satan ended in issue #21 (Nov. 1941), her place taken in #22 (Dec. 1941) by the first appearance of one of the biggest-selling[13] comics characters of the 20th century, Archie Andrews, and what would become the core of his group of friends: Jughead and Betty Cooper.

[16] On a lighter note, issue #31 (Sept. 1942) had "Sergeant Boyle" visiting the MLJ offices after he had failed to send them details of his latest exploits for them to publish, while #34 (Nov. 1942) contained a one-page text piece, 'Meet the Editor', about Harry Shorten.

"Bentley of Scotland Yard" ended in #41 (August 1943), replaced by the slapstick voyages of "Marco Loco, Adventurer" (#42–52) by Carl Hubbell.

The Hangman ended in #47 (March 1944), and although he was replaced by another costumed character, Black Hood in #48 (April 1944),[19] the humor continued to take over.

Li'l Jinx arrived in #62 (July 1947), replacing Black Hood—who had made two final appearances in #59–60 and revealed his identity to the world, becoming a detective.

All these humor strips would continue in Pep Comics for years, Katy Keene running until #154, although Bill Woggon had stopped drawing her with #126, and Li'l Jinx staying to the end.