Her visit to Nigeria, Africa's most populous nation and a major supplier of US oil imports, came as President Goodluck Jonathan is under growing pressure to stop the violence in the northern and central regions of the country.
Islamist militant group Boko Haram has killed more than 1,400 people since 2010, according to Human Rights Watch.
Clinton said after meeting Jonathan, key ministers and security chiefs on the latest stop of her African tour that "we really believe that the future for Nigeria is limitless.
"But the most important task that you face, as you have said, is making sure that there are better opportunities for all Nigerians -- north, south, east, west," she said.
US diplomats have repeatedly spoken of the deep poverty in Nigeria's north that many say has fed the insurgency.
"We want to work with you and we will be by your side as you make the reforms and take the tough decisions that are necessary," Clinton added.
She mentioned efforts to improve transparency and limit corruption in a country consistently ranked as one of the world's most graft-ridden. She also spoke of US help in improving agriculture -- a key concern for Nigeria's north.
Ahead of the meeting, a State Department official said Clinton would also offer help to Nigeria in boosting the country's investigative and intelligence capabilities.
"This is a problem for Nigeria, but also, northern Nigeria borders Cameroon, it borders Niger," the official said, expressing concern that a radical network could undermine the security of neighbouring states.
The US offer of assistance included helping to develop Nigeria's forensics and investigative procedures, according to the official.
"We can help them develop mechanisms for tracking and determining individuals who are likely to be engaged in supporting Boko Haram actively," the official said.
Washington would also be willing to help Nigeria develop an intelligence coordination centre that would assist the country in integrating information, the official said.
Some US lawmakers have been pushing President Barack Obama's administration to label Boko Haram a terrorist group, but diplomats have resisted the designation, stressing the group remains domestically focused.
In June however, the United States labeled suspected Boko Haram leader Abubakar Shekau and two other Nigerian militants "global terrorists", allowing any US assets they may have to be blocked.
Shekau appeared in a video posted to YouTube last weekend dismissing the designation and criticising Jonathan.
Nigeria has provided some eight percent of US oil imports, and crude production, based in the country's south, has not been affected by the insurgency.
Boko Haram's targets have continually widened, with the group having moved from assassinations to increasingly sophisticated bombings, including suicide attacks.
Members are believed to have sought training in northern Mali from Al-Qaeda in the Islamic Maghreb, Al-Qaeda's north African branch, and Western nations have been monitoring closely for signs of further links.
Boko Haram has attacked UN headquarters in the capital Abuja and one of the country's most prominent newspapers, in addition to frequent bombings and shootings in the northeast, where the sect is based.
While Muslims have often been its victims, it has recently specifically targeted churches, and Jonathan has accused the group of seeking to provoke a religious crisis in a country roughly divided between a mainly Muslim north and predominantly Christian south.
The group is believed to include a number of factions with varying interests, and many analysts say deep poverty and a lack of development in Nigeria's north have been key factors in creating the insurgency.
A senior US official said Thursday that Washington wants to encourage Nigeria to set up a "comprehensive programme in the north" that would combine a security strategy with a socio-economic plan.
The country and its enormous economic potential have long been held back by deeply rooted corruption, with infrastructure sorely lacking and electricity blackouts occurring daily despite its oil wealth.
Clinton was to travel to Ghana next for Friday's funeral of president John Atta Mills, who died on July 24. She was also due to briefly visit Benin on Friday as the last stop on her African tour.