Mohammed Reza Alizamani and Arash Rahmani were hanged on Thursday, having been sentenced to death in mass trials.
"The European Union strongly condemns these two executions and expresses its profound concern at the death sentences imposed on persons tried in these mass trials," High Representative Catherine Ashton said in a statement.
The EU "opposes the death penalty, whatever the circumstances," she added. "It calls on the Iranian authorities to suspend the sentences passed and to declare a moratorium on all forms of capital punishment."