Speaking in Geneva, Margaret Chan said the WHO had been overwhelmed by the epidemic in West Africa.
She said the demands were more than 10 times greater than anything else it had experienced.
The Ebola outbreak was first reported in March 2014 and is believed to have claimed more than 11,000 lives.
The WHO and Ms Chan had faced criticism for the slow international response to the epidemic.
“With the support of member states, I am establishing a $100m contingency fund, financed by flexible voluntary contributions, to ensure we have the necessary resources available to immediately mount an initial response,” Ms Chan told WHO’s annual meeting.
She also said that, among other measures, she was putting in place a new “unified” programme to help deal with health emergencies.
“I do not ever again want to see this organisation faced with a situation it is not prepared, staffed, funded, or administratively set up to manage,” she said.
“We will move forward on an urgent footing. I plan to complete these changes by the end of the year.”
Ms Chan added that the Ebola outbreak “shook this organisation to its core” but she hoped the reforms would help give it “new relevance and empower it to lead in global health”.
Earlier, German Chancellor Angela Merkel told the annual meeting’s opening session that the organisation had to streamline its management to respond quickly to crises like Ebola.
“We ought to have reacted far earlier,” she said.
“I am convinced that if we act faster and have a clear command structure in place, we will be better equipped to combat a crisis like Ebola next time that happens.”
The Ebola outbreak was the deadliest occurrence of the disease since its discovery in 1976.
The first confirmed cases occurred in south-eastern Guinea early last year and spread to Liberia, Sierra Leone, Nigeria and Mali. –BBC