In a statement, the NFF described it as an "historic and binding agreement that will eliminate all manner of rancour and distractions around Nigeria's preparation and participation" at the World Cup in Russia next year.
Nigeria, who have qualified for their sixth World Cup, have reached the round of sixteen three times and been eliminated in the group stage twice.
The Super Eagles were involved in a protracted dispute ahead of the 2013 Confederations Cup in Brazil and a bonus row also disrupted their World Cup campaign the following year, prompting the players to boycott a training session.
Similar problems have affected other African teams.
Ghana's players refused to train over a pay dispute at one point during the last World Cup and around $3 million in cash eventually arrived in Brasilia with a convoy of cars bringing the money to the team's headquarters.
NFF director Shehu Dikko said no stone had been unturned this time.
"Every detail has been agreed on, match bonus for each match and each round up to the Final as well as share of income from FIFA money for each round until the stage we are able to get to at the finals," he said.
"We also agreed on preparation, such as how much players will be paid for the friendly matches, including how and when the monies would be paid.
"We even delved into how the NFF would apply the funds due to it from FIFA after paying the players their share."
He said the agreement would be "a catalyst for the Super Eagles' best performance ever at the FIFA World Cup."
The agreement was also signed by coach Gernot Rohr and team captain John Obi Mikel, among others, the NFF said.
"We are very happy and excited with this development," said Obi Mikel.
"This is the first time since I started playing for the senior team that I would see everything regarding preparation and bonuses and allowances put down in black and white and a binding agreement executed."
(Writing by Brian Homewood; Editing by Christian Radnedge)
