Duncan, Lee and other top school officials held a roundtable discussion during a visit to Everett Middle School, one of nine schools in San Francisco that was awarded federal School Improvement Grants in 2011.
The historically low-performing schools in the city's Mission and Bayview districts were given $45 million over a three-year period that went toward professional development and coaching for school staff, among other improvements, according to school district officials.
Since 2008, those nine schools have had an 18.4 percent gain in English language arts proficiency and a 26.9 percent gain in math proficiency, district officials said.
Duncan said he was "absolutely inspired" by the improvements made at Everett.
He said during today's visit, he talked to an eighth-grader there who "said she was terrified to come to this school as a sixth grader, and now this school has a wait list."
Lee said the federal funding has helped reduce barriers for low-income students and those who speak English as a second language.
"Once we get rid of those barriers, our kids who come from all over the world will compete on an international basis," he said.
Duncan said he is working to get more federal funding from Congress, but "they look at education as an expense instead of an investment."
He said in the meantime, San Francisco can come up with creative ways to maintain funding for the schools, noting that the mayor has sought help from the private and nonprofit sectors.
"People want to be part of a winner," Duncan said. "We've gotten something started and he's got a heck of a story to tell."
The federal School Improvement Grant funding ends this September.
The other schools in San Francisco that received the funding are Bryant Elementary, Cesar Chavez Elementary, George Washington Carver Elementary, Buena Vista Horace Mann K-8, John Muir Elementary, John O'Connell High, Mission High and Paul Revere K-8.