Bobby Smith from Stevenage and James Dennis from Gloucestershire climbed onto the roof of the historic church in a demonstration for the group New Fathers4Justice.
The protest took place on Sunday evening, Father's Day.
Banners were left hanging from scaffolding which said "Parental Alienation", "Give me back Elmo" and "Daddy's not giving up on you Elmo x x x".
Mr Smith told the Press Association: "We chose Westminster Abbey because it's such an iconic church.
"And because it's Father's Day - we haven't just done this on the spur of the moment.
"I have got two kids and I have no access at all to them. I haven't seen one of them for over two years, and before that it was supervised contact.
"Fathers' rights just aren't on the political agenda.
"Kids are much worse off without their fathers around. We can't sit back and let our children grow up without us."
The two men agreed to climb down off the Abbey after several hours.
Two men scale Westminster Abbey in a Father's Day protest: http://t.co/JxsJgnukh9 by @kateferguson4 pic.twitter.com/Ma6NQrg5PU
— Press Association (@PA) June 21, 2015