CraveOnline gave the season a rating of 8.0 out of 10, and spoke highly of its "little pieces of continuity", "sharp parody", and "non sequitur gags".

[48] Entertainment Focus gave it 4 out of 5 stars, concluding "Some people have criticised The Simpsons claiming that the show is tired and has passed its prime.

[49] High-Def Digest also gave a 4/5 star rating, saying "As mentioned in the review, there are plenty of laughs to be had in this season, but very few of them come from a place that feels truly genuine and sincere.

[51] DVDTalk wrote "The Simpsons: Season Sixteen isn't the best of the series' run but it is a very strong collection of truly funny and frequently quite clever doses of animated comedic insanity.

[56] In 2005, "On a Clear Day I Can't See My Sister" was nominated for the Best Television Episodic Comedy Environmental Media Award.

In the same year, Matt Warburton was nominated for Writers Guild of America Awards for animation as well for "The Father, the Son, and the Holy Guest Star".

[55] The DVD and Blu-ray box set for season sixteen was released by 20th Century Fox Home Entertainment in the United States and Canada on Tuesday, December 3, 2013, eight years after it had completed broadcast on television.

The boxart features Professor Frink, and a special limited edition "embossed head case" package was also released.