On January 7, 2011, Puella Magi Madoka Magica debuted on Mainichi Broadcasting System (MBS), Tokyo Broadcasting System (TBS), and Chubu-Nippon Broadcasting (CBC) in Japan. The first ten episodes aired weekly without interruption and were made available for streaming on Nico Nico Douga and BIGLOBE's Anime One service. That March, the planned broadcasts of the last two episodes were halted because of the 2011 Tōhoku earthquake and tsunami; TBS also canceled its scheduled airing of the 10th episode so it could provide more news coverage of the natural disaster.

Urobuchi apologized to viewers for the delays; he also said the postponements could be viewed in a positive light because they alleviated some production pressures on animation studio Shaft because of the tight broadcast schedule. Citing particularly challenging drawings for episodes 11 and 12, Urobuchi and Iwakami planned to have Shaft continue to improve the episodes up until their rescheduled broadcasts. According to Urobuchi if episode 11 had been aired in its current state as scheduled, the result would likely have been disappointing. On March 23, 2011, the broadcast for the rest of the series was indefinitely delayed but the production team reported that they were continuing to work on the episodes and announced their intention to finish airing the series by April. On April 10, 2011, the official website for Puella Magi Madoka Magica announced that broadcasts would resume on April 21. Episodes 11 and 12 aired back-to-back on MBS while TBS and CBC ran episode 10 together with episodes 11 and 12.

Iwakami later commented on this unique production experience in an interview with Anime News Network. He said Shaft was always pressed for time during the production process and only just completed each episode before its air time. After the earthquake and tsunami, he stated that many of the company's staff were upset by the incident and were unable to work effectively on episodes 11 and 12. He said, however, "a week went by, and two weeks went by, and the staff started saying that they couldn't stay in shock forever, that they had to keep on going, and then production continued". The series was released on six Blu-ray Disc (BD) and DVD volumes between April 27 and September 21, 2011, having been delayed by the earthquake from the original release date of March 30, 2011. Drama CDs were included with the first, third, and fifth BD/DVD volumes. The sixth and final volume released on September 21, 2011, contains a director's edit of episode 12. The series began streaming on Crunchyroll on February 15, 2012, as well as on Hulu and Crackle.

Aniplex of America released the series in North America, including an English dub, in three BD and DVD volumes released between February 14 and June 12, 2012. Aniplex also released limited editions containing the original soundtrack CDs and special items. Manga Entertainment licensed the series in the United Kingdom and released it on October 29, 2012 on BD and DVD in a complete collection. Madman Entertainment licensed the series in Australia, where it was broadcast on the children's channel ABC Me on June 29, 2013, following an early preview on January 6. The dubbed series began streaming on Viz Media's streaming service Neon Alley in late 2013. In Italy, the series was broadcast on Rai 4 on February 5 until April 22, 2012. On September 1, 2018, a television anime series based on the smartphone game Magia Record was announced. It was originally scheduled to begin airing in 2019, but it was delayed to a January 2020 premiere. It began airing on January 4, 2020.