The album was released to widespread acclaim, and was hailed by critics as a departure from their previous guitar-heavy alternative rock sound into a more layered, intricately arranged work.

[24] The Soft Bulletin is considered by some to be partially responsible for establishing the latter-day identity of the Flaming Lips, and as its following expanded over the years after its release, paving the way to their being among the most well-respected groups of the 2000s.

In 2006, Robert Dimery chose The Soft Bulletin and its follow-up Yoshimi Battles the Pink Robots as part of his book 1001 Albums You Must Hear Before You Die.

AllMusic's Jason Ankeny gave it a highly enthusiastic review, concluding that "there's no telling where The Lips will go from here, but it's almost beside the point – not just the best album of 1999, The Soft Bulletin might be the best record of the entire decade".

In addition, many people who sent their incorrect CDs in for replacement also received a handwritten letter of apology from the band's bassist, Michael Ivins.