“We are sticking to the agreement with Iran,” Juncker said while addressing the Austrian parliament in Vienna on Friday.
He added that the EU was engaged in "intensive talks" with the Americans about the deal, officially known as the Joint Comprehensive Plan of Action (JCPOA).
Juncker further said the bloc needed to strengthen its role in the world and urged member states to take the required steps to the same effect.
"We have locked ourselves in the darkroom of unanimity," he said, stressing that EU needed to abandon the requirement for unanimity when deciding on foreign policy issues.
Iran signed the JCPOA with the permanent members of the UN Security Council - the US, Britain, France, Russia and China - as well as Germany in 2015. Based on it, Iran agreed to restrict certain aspects of its nuclear energy activities in return for the removal of nuclear-related sanctions against the country.
Back in May, US President Donald Trump pulled Washington out of the JCPOA despite objections from other parties.
Besides re-imposing the anti-Iran sanctions it had lifted under the accord, the Trump administration has also been seeking to discourage European firms from doing business with Iran by threatening them with penalties.
However, the other signatories have vowed to try and protect their business links with Iran in face of US sanctions and keep the JCPOA alive.
Iran has stayed in the deal but has stressed that the other parties to the agreement have to work to offset the negative impacts of America's withdrawal if they wanted Tehran to continue to remain in it.
Europe has been taking a range of measures to meet Iran's demand for practical guarantees.
On Monday, Iran’s Foreign Ministry Bahram Qassemi said the country had been doing copious work with Europe to devise a mechanism to guarantee continued bilateral trade despite attempts by the US to obstruct such cooperation.