But Michel Barnier made it clear that Brussels has no plans to renegotiate the divorce deal it signed with Johnson's predecessor Theresa May in November last year.
"It's a very important moment for the Brexit. We look forward to hearing what the new prime minister Boris Johnson wants. What are the choices of the UK? Is it an orderly Brexit?" Barnier told the BBC.
"The 'no deal' will never be the choice of the EU, but we are prepared... we will work all along the next few weeks or months with the new UK government in the best possible way, in a very constructive spirit to facilitate the ratification of the withdrawal agreement."
Asked what he thinks of Johnson, who has demanded the deal be reopened, Barnier said he had only met him once, at the opening ceremony of the 2012 London Olympics, and added: "We will work with him. I think he is clever."
Earlier, Barnier had briefed the European Parliament's Brexit steering group, under former Belgian premier Guy Verhofstadt. The MEPs also stuck to Brussels' line that the withdrawal agreement will not be renegotiated.
"This is our position it is impossible to change our position," group member Antonio Tajani told reporters.
But the MEPS reiterated that they would support EU leaders if they decide to rewrite an accompanying non-binding political declaration to seek "a more ambitious future EU-UK partnership".
A closer future relation could ensure "the Irish backstop would not be necessary", the group's statement said. Johnson insists the backstop must be removed from the withdrawal agreement, an idea rejected by EU capitals.
The group congratulated Johnson, but warned that recent statements, not least those made during the Conservative Party leadership campaign, have greatly increased the risk of a disorderly exit of the UK.
And they warned that a disorderly or no-deal Brexit -- which Johnson has said he will pursue if the deal is not rewritten before October 31 -- would be "very damaging".
"Such an exit will not be mitigated by any form of arrangements or mini deals between the EU and the UK."
The Brexit Steering Group "recalls that there is no transition period without a withdrawal agreement," it said.