Four Republicans joined Democrats to defeat Boebert's amendment, though the House approved two other anti-transgender measures.
The proposed provisions would ban Pride flags at federal buildings and restrict funding tied to LGBTQ rights and gender-affirming care.
The president's executive order prohibits federal funds from being spent by institutions providing gender-affirming care to people under 19.
Congressional lawmakers passed a military funding bill banning TriCare from covering transgender health treatments for minors.
Senator Joe Manchin sides with Republicans to approve amendments aimed at making it more difficult for trans military members to transition.