Speaking to reporters in the Oval Office, Trump said: "There's a massive deficit that we have with Ireland... we want to sort of even that out as nicely as we can, and we'll work together."
Martin told President Trump that foreign investment is a two-way street, adding that Ireland is "investing a lot more in America now".
'Ireland has entire US pharmaceutical industry in its grasp' - Trump
The EU's move is in retaliation to President Trump's 25% tariffs on all steel and aluminium imports into the US, which came into effect overnight.
Trump said it had caused "ill will".
"The European Union's been very tough, and it's our turn too. We get a turn at that also," he said.
"I'm not knocking it, they are doing what they are doing for the EU, but it does create ill will and you know we are going to do reciprocal tariffs," he added.
'We don't want to do anything to hurt Ireland'
Martin arriving at the White House for a meeting with Donald Trump
Official figures from Ireland's statistics agency suggest the country had a goods-trade surplus with the US of just over €50bn (£41.6bn) in 2024.
Ireland's goods exports to the US were €72.6bn (£60.4bn) in 2024 while its imports from the US were €22.5bn (£18.7bn).
Trump said that the EU was "set up in order to take advantage of the United States".
When asked if Ireland was also taking advantage of the US, Trump said: "Of course."
"I have great respect for Ireland, for what they did and they should have done just what they did. But the United States shouldn't have let that happen. We had stupid leaders, we had leaders who didn't have a clue."
He added: "All of a sudden Ireland has our pharmaceutical companies, this beautiful island of five million people has got the entire US pharmaceutical industry in its grasps.
"The Irish are smart, smart people and you took our pharmaceutical companies - and other companies - but you know, through taxation, proper taxation, they made it very, very good for companies to move up there," he added.
Trump also said that if he drained Ireland of all the US companies "maybe I'd lose the Irish vote".
"We don't want to do anything to hurt Ireland, but we do want fairness and [Martin] understands that," he added.
However, Martin said the pharmaceutical companies "are doing very well in Ireland", and that there was room to discuss a deal.
"I think there's room for those companies to grow in America and many of them, by the way, have already announced fairly significant manufacturing investments now [in the US]," the taoiseach added.
Martin said Ireland had served the US companies well with a strong, educated workforce and access to the EU single market.
Housing answer stirs controversy
The president said Ireland's housing crisis was caused by the country "doing so well".
Housing availability and cost is a major political and social issue in Ireland, with reports stating thousands of new homes every year are needed to keep up with demand.
"You know why they have a housing crisis? Because they're doing so well, they can't produce houses fast enough," Trump said.
Martin added it was a "good answer".
However the remark has drawn criticism from opposition parties, with Sinn Féin stating that joking about the housing crisis is "never a good answer".
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Trump also praised Northern Ireland golfer Rory McIlroy and MMA fighter Conor McGregor during the visit.
He called McIlroy "talented", adding he had played a round with him three weeks ago.
The president also complimented McGregor's tattoos: "He's got the best tattoos I've ever seen".
Trump 'unaware' of boycott
Earlier, the US president said he was unaware that some political parties were boycotting St Patrick's Day celebrations at the White House.
Sinn Féin, the Social Democratic and Labour Party (SDLP) and Alliance all ruled out attending events in Washington over the Trump administration's stance on Gaza.
When asked about the boycotts, Trump replied: "I haven't heard that, I really haven't heard that."
After the bilateral meeting, both Trump and Martin travelled to Capitol Hill to attend the Friends of Ireland luncheon hosted by the US House speaker, Mike Johnson.
Micheál Martin addressed the Friends of Ireland luncheon on Wednesday afternoon
Asked for his reaction to Trump being unaware some parties had decided to boycott events, Martin said: "I'm not going to comment on that.
"I note that there was a strong presence in Northern Ireland at the lunch. I saw Hilary Benn there, the Northern Secretary of State," he told reporters.
Addressing the luncheon, Martin said Trump is a "great friend of Ireland" and "we hope to welcome you back to our small island... very soon".
The United States has been a "place of welcome and opportunity for Irish people" for centuries, the taoiseach added.
"Our nation's green has been threaded through the rich tapestry of the United States by almost 32 million Irish-Americans."
Also speaking at the event, Trump said the "Irish spirit is truly alive and thriving in America".
The president met Deputy First Minister Emma Little-Pengelly, Northern Ireland Assembly Speaker Edwin Poots and Communities Minister Gordon Lyons.
O'Neill 'should have been here'
Democratic Unionist Party (DUP) Deputy First Minister Emma Little-Pengelly met Trump in Washington
Speaking to BBC Newsline after the meeting, Little-Pengelly said she had a good conversation with the president about the US and NI's "long-standing relationship" and his keenness to work together.
However, she added, Sinn Féin First Minister Michelle O'Neill "should have been here".
"I'm sure Michelle O'Neill would say she doesn't think that I should have been here but of course it's a joint office and I'm here representing the Northern Ireland government," she said.
"I believe that it's incredibly important to show up, turn up and speak up and that's the key thing that I will always do."
US 'steadfast friend' of Ireland
Prior to the meeting, Martin attended a breakfast hosted by Vice-President JD Vance.
Speaking at the breakfast he said that the US "has been a steadfast friend of Ireland for centuries".
He said the peace process was a "signature achievement of US foreign policy", adding that Ireland is "ready to play our part in supporting work to end conflict and to secure peace in the Ukraine or in the Middle East or wherever".
Martin welcomed the "progress that has clearly been made" as a result of the Trump administration's "unrelenting focus and effort" to secure peace.
US Vice-President JD Vance and Second Lady Usha Vance welcome Micheál Martin and his wife Mary O'Shea to their residence in Washington DC
Vance described the US-Ireland relationship as "one of the great alliances and great friendships between nations".
He added that Ireland is a country with "incredible community… beautiful landscape and also a lot of interesting technological growth".
"One of the more robust areas for us to work on with our Irish friends in the years to come is going to be technology and particularly artificial intelligence," he said.
JD Vance said Ireland was a country with "a lot of interesting technological growth"
The taoiseach was the first EU leader to return to the Oval Office since the president's bust-up with Ukraine President Volodymyr Zelensky.
The bilateral meeting came amid heightened concern over the future of Ireland's economy, which is heavily reliant on US multinationals.
Trump sees this as a trade imbalance and is keen to entice those companies back to the US.
However, Martin said he would use his visit to the Oval Office to highlight an "increasingly two-way" trade and investment relationship.
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Speaking ahead of Martin's visit to the Oval Office, Democrat member of the House of Representatives Brendan Boyle told BBC News NI's The View that "what the Trump administration is doing with respect to tariffs makes no economic sense, and it makes no sense in terms of our national security".
Boyle said that imposing tariffs on Canada suggests that no country is "safe fully from this sort of madness", including Ireland.
Congressman Brendan Boyle says Trump's tariffs "make no sense"
He added that Martin should "remind President Trump that Ireland, despite its small size, is one of the largest investors in the United States and one of the largest job creators in the United States".
"On the one hand, [Trump] likes to say, you know, we're the best, he's the best, He's the greatest. Everything is a superlative.
"But then in the next breath, he says, we're suckers, we're losers, we're being taken advantage of by every other country."
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