The UK and the US will jointly fund a counter-terrorism police unit in Yemen following the alleged failed bomb airline attack over Detroit.
Downing Street and the White House said they would also "intensify" efforts to tackle the emerging threat in Somalia.
It is widely believed the alleged Christmas Day bomber, Nigerian Umar Farouk Abdulmutallab, was armed and trained by Yemen-based al-Qaeda.
The US' top Middle East general has also met with the president of Yemen.
Gen David Petraeus - who is responsible for US Middle East and Central Asian operations - reportedly said the US was keen to support Yemen's fight against al-Qaeda.
On Saturday, Mr Obama for the first time publicly accused an offshoot of al-Qaeda, based in Yemen, over the alleged plot.
A statement from No10 said Mr Brown and US President Barack Obama had discussed "increased UK-US working" in a series of phone calls since the alleged failed plot on Christmas Day.
Mr Brown has called Yemen "both an incubator and potential safe haven for terrorism" and said it presented "a regional and global threat".
The UK is one of Yemen's leading donors and is already helping to train counter-terrorism officials in the country.
The increased assistance from both the UK and US will include support for the Yemeni coastguard operation.
Downing Street told the BBC: "This is a decision reached after discussion with the Yemeni government and the White House.
"The details are still to be worked out but this will build on the work already being done by the UK to help the Yemeni government combat terrorism."
Gen David Petraeus flew to Yemen to discuss stepping up co-operation between the two countries in the fight against al- Qaeda, according to the Yemeni state news agency.
It says Gen Petraeus met President Ali Abdallah Saleh in the capital Sana'a and handed over a letter from President Obama.
The BBC's world affairs correspondent Caroline Hawley said there had been growing concern for some time about al-Qaeda exploiting Yemen's troubles to establish a safe haven in the country's ungoverned spaces.
"But the failed bomb attack last week has put the international spotlight on the Arab world's poorest country," she added.
On Tuesday, Yemen's Foreign Minister Abu Bakr al-Qirbi told the BBC that Yemen had the will and ability to deal with al-Qaeda, but needed more support from the West.
"We need more training," he said.
"We have to expand our counter-terrorism units and this means providing them with the necessary training, military equipment, ways of transportation - we are very short of helicopters."
In Somalia, the prime minister and president believe a larger UN peacekeeping force is required.
Somalia has not had a functioning central government since 1991.
Rival Islamist factions are battling forces loyal to the weak UN-backed government, which controls only small parts of the capital Mogadishu.
One of these groups, al-Shabab, is viewed by the Americans as al-Qaeda's proxy in Somalia.
The alleged bomber, Mr Abdulmutallab, who is now in US custody, is accused of trying to detonate a bomb on a flight as it came in to land.
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