| Award | Date of ceremony | Category | Recipient | Result | Ref. |
| American Cinema Editors Eddie Awards | March 14, 2025 | Best Edited Limited Series | Henk van Eeghen (for "After Hours") | Nominated | |
| American Film Institute Awards | December 5, 2024 | Top 10 TV Programs of the Year | The Penguin | Won | |
| American Society of Cinematographers Awards | February 23, 2025 | Outstanding Achievement in Cinematography in Motion Picture, Limited Series, or Pilot Made for Television | Jonathan Freeman (for "Homecoming") | Nominated | |
| Art Directors Guild Awards | February 15, 2025 | Excellence in Production Design for a Television Movie or Limited Series | Kalina Ivanov | Won | |
| Astra TV Awards | June 10, 2025 | Best Limited Series | The Penguin | Nominated | |
| Best Actor in a Limited Series or TV Movie | Colin Farrell | Won |
| Best Actress in a Limited Series or TV Movie | Cristin Milioti | Won |
| Best Supporting Actor in a Limited Series or TV Movie | Clancy Brown | Nominated |
| Best Supporting Actress in a Limited Series or TV Movie | Deirdre O'Connell | Nominated |
| Best Cast Ensemble in a Limited Series or TV Movie | The Penguin | Won |
| Best Directing in a Limited Series or TV Movie | Helen Shaver (for "Cent'Anni") | Nominated |
| Best Writing in a Limited Series or TV Movie | Lauren LeFranc (for "A Great or Little Thing") | Nominated |
| Cinema Audio Society Awards | February 22, 2025 | Outstanding Achievement in Sound Mixing for Non-Theatrical Motion Pictures or Limited Series | Christof Gebert, Andy Kris, Rich Bologna, and Mark DeSimone (for "After Hours") | Nominated | |
| Critics' Choice Super Awards | August 7, 2025 | Best Superhero Series, Limited Series or Made-for-TV Movie | The Penguin | Won | |
| Best Actor in a Superhero Series, Limited Series or Made-for-TV Movie | Colin Farrell | Won |
| Best Actress in a Superhero Series, Limited Series or Made-for-TV Movie | Cristin Milioti | Won |
| Best Villain in a Series, Limited Series or Made-for-TV Movie | Colin Farrell | Won |
| Critics' Choice Television Awards | February 7, 2025 | Best Limited Series | The Penguin | Nominated | |
| Best Actor in a Limited Series or Movie Made for Television | Colin Farrell | Won |
| Best Actress in a Limited Series or Movie Made for Television | Cristin Milioti | Won |
| Best Supporting Actress in a Limited Series or Movie Made for Television | Deirdre O'Connell | Nominated |
| Directors Guild of America Awards | February 8, 2025 | Outstanding Directing – Miniseries or TV Film | Kevin Bray (for "Top Hat") | Nominated | |
| Helen Shaver (for "Cent'Anni") | Nominated |
| Jennifer Getzinger (for "A Great or Little Thing") | Nominated |
| Golden Globe Awards | January 5, 2025 | Best Television Limited Series, Anthology Series, or Motion Picture Made for Television | The Penguin | Nominated | |
| Best Performance by a Male Actor in a Limited Series, Anthology Series, or a Motion Picture Made for Television | Colin Farrell | Won |
| Best Performance by a Female Actor in a Limited Series, Anthology Series, or a Motion Picture Made for Television | Cristin Milioti | Nominated |
| Golden Reel Awards | February 23, 2025 | Outstanding Achievement in Sound Editing – Broadcast Long Form Dialogue and ADR | Rich Bologna, Lawrence Zipf, Angela Organ, Tony Martinez, and Michael McMenomy (for "Cent'Anni") | Nominated | |
| Outstanding Achievement in Sound Editing – Broadcast Long Form Effects and Foley | Rich Bologna, Lawrence Zipf, Diego Perez, Wyatt Sprague, Matt Haasch, and Gareth Rhys Jones (for "After Hours") | Nominated |
| Outstanding Achievement in Music Editing – Broadcast Long Form | Ben Holiday, Chad Birmingham, and Luke Dennis (for "Cent'Anni") | Won |
| Golden Trailer Awards | May 29, 2025 | Best Drama (Trailer/Teaser) for a TV/Streaming Series | HBO / Mocean (for "Untouchable") | Nominated | |
| Best Drama (TV Spot) for a TV/Streaming Series | HBO / Bond (for "Hype") | Nominated |
| Best BTS/EPK for a TV/Streaming Series (Over 2 minutes) | HBO / Marketing AV (for "Becoming The Penguin") | Won |
| Gotham TV Awards | June 2, 2025 | Outstanding Lead Performance in a Limited Series | Cristin Milioti | Nominated | |
| Independent Spirit Awards | February 22, 2025 | Best Lead Performance in a New Scripted Series | Cristin Milioti | Nominated | |
| Irish Film & Television Awards | February 14, 2025 | Best Lead Actor (Television) | Colin Farrell | Won | |
| Best Cinematography | Darran Tiernan | Nominated |
| Make-Up Artists and Hair Stylists Guild Awards | February 15, 2025 | Best Contemporary Make-Up in a Television Series, Television Limited or Miniseries or Television New Media Series | Martha Melendez, Kim Collea, Maria Maio, and Mia Bauman | Nominated | |
| Best Contemporary Hair Styling in a Television Series, Television Limited or Miniseries or Television New Media Series | Brian Badie, Jenn Vasilopoulos, Mariko Miyagi, and Bobby Diehl | Nominated |
| Best Special Make-Up Effects in a Television Series, Television Limited or Miniseries or Television New Media Series | Mike Marino, Michael Fontaine, Crystal Jurado, Diana Y. Choi, and Claire Flewin | Won |
| NAACP Image Awards | February 22, 2025 | Outstanding Hairstyling | Brian Badie | Nominated | |
| Primetime Emmy Awards | September 14, 2025 | Outstanding Limited or Anthology Series | Lauren LeFranc, Matt Reeves, Dylan Clark, Craig Zobel, Colin Farrell, Bill Carraro, Daniel Pipski, Vladimir Cvetko, Erika L. Johnson, Noelle Valdivia, John McCutcheon, Nick Towne, Corina Maritescu, Claudine Farrell, and Dana Robin | Nominated | |
| Outstanding Lead Actor in a Limited or Anthology Series or Movie | Colin Farrell | Nominated |
| Outstanding Lead Actress in a Limited or Anthology Series or Movie | Cristin Milioti | Won |
| Outstanding Supporting Actress in a Limited or Anthology Series or Movie | Deirdre O'Connell | Nominated |
| Outstanding Directing for a Limited or Anthology Series or Movie | Jennifer Getzinger (for "A Great or Little Thing") | Nominated |
| Helen Shaver (for "Cent'Anni") | Nominated |
| Outstanding Writing for a Limited or Anthology Series or Movie | Lauren LeFranc (for "A Great or Little Thing") | Nominated |
| Primetime Creative Arts Emmy Awards | September 6, 2025 | Outstanding Casting for a Limited or Anthology Series or Movie | Cindy Tolan and Suzanne Ryan | Nominated |