The album debuted at #1 on the Canadian Albums Chart, and stayed at #1 for four straight weeks. The album has been certified 5x platinum in Canada. By March 1997, the album had sold 650,000 units in Canada. It peaked at No. 134 on the Billboard 200. Trouble at the Henhouse peaked at #80 in the Netherlands.
The Encyclopedia of Popular Music deemed the album "reliably melodic."The Washington Post wrote that "a surprisingly large number of these songs are more atmospheric than aggressive."Trouser Press wrote that "too much of Henhouse finds the Hip wallowing in meandering psychedelica, and too many of the slower songs ('Sherpa,' 'Flamenco,' 'Put It Off') sound too much alike." The Orlando Sentinel praised Gord Downie's ability to pen lyrics that "found beauty in the tiny wonders of life while exploring big questions of existence."