Emanuel will sign an agreement between the University of Chicago and Ben-Gurion University on Sunday at the home of Israeli President Shimon Peres.
The schools will work with Argonne Lab on projects to improve drinking water.
Meanwhile, some Chicagoans have questioned the timing of Emanuel's trip overseas.
Emanuel's trip coincided with one of the most eventful weeks for Chicago Public Schools. Over 50 CPS schools closed their doors for goods while hundreds of teachers were laid off.
A spokeswoman said the mayor's trip was scheduled months ago for his daughter's bat mitzvah. But critics say they remember last March, when the CPS school closings list was announced and the mayor was on a family ski trip in Utah.
Emanuel and his family will return to Chicago on Monday.