Mogherini said the European Union delegation will keep its embassy in Tel Aviv and continue to respect UN resolutions opposing Israel's annexation of east Jerusalem, which the Palestinians want as the capital of a future state.
"I believe that it is very important for us all to refrain from unilateral actions, especially those that have serious consequences in large sectors of public opinion in large parts of the world," Mogherini told a press conference when asked about Trump's stated plans.
In a break with previous administrations, US president-elect Trump has pledged to recognise Jerusalem as Israel's capital and relocate the US embassy there from Tel Aviv.
Mogherini said at first she could not answer a hypothetical question when Trump does not actually enter office until Friday and no decision has been taken yet on moving the embassy.
But she added: "For sure I'm worried that large parts of public opinion in parts of the world that are quite significant -- the Arab world but also Africa, Asia and parts of Europe -- could have in reaction of a move that for sure would not be in line with ... the international consensus."
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She cited the consensus embodied in UN Security Council resolution 478 of 1980 which opposed Israel's annexation of east Jerusalem as part of its undivided capital.
Israel captured east Jerusalem during the 1967 war and later annexed it -- in a move not recognised by the international community -- declaring all of the city its unified capital.
"When it comes to Jerusalem, the European Union will continue to respect the international consensus embodied in UN Security Council resolution 478 of 1980," the former Italian foreign minister said.
"We will for sure not move our delegation that is in Tel Aviv," she said.
Mogherini also described the weekend Middle East peace conference in Paris as "useful" for reconfirming international support for a two-state solutions, even if neither the Israelis or Palestinians attended.
The Palestinians welcomed the gathering for calling for the end to the Israeli occupation, but Israel dismissed it as "futile" and warned it would hamper the prospects of peace.