"The United States is focused on reaching a comprehensive deal with Iran that prevents Iran from acquiring a nuclear weapon and verifiably assures the international community of the exclusively peaceful nature of its nuclear program," the White House said in a statement.
"The president underscored the United States' enduring commitment to the security of Israel and the importance of continuing close cooperation with Israel on this issue."
The leaders spoke by telephone ahead of a meeting between Secretary of State John Kerry and his Iranian counterpart later this week, in which the US top diplomat hopes to accelerate the so-called P5+1 talks between Iran and Britain, China, France, Russia and the United States plus Germany.
Under an interim deal, Iran's stock of fissile material has been diluted from 20 percent enriched uranium to five percent in exchange for limited sanctions relief.
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However, two deadlines for a final deal have been missed, and a third on July 1 is looming.
During the phone call, Obama also "underscored that the United States does not believe Palestinian accession to the ICC is a constructive way forward," the White House said.
On Wednesday, the Palestinians formally joined the International Criminal Court, drawing fresh opposition from Washington, a close ally of the Jewish state.
"President Obama reiterated the United States' position that the Palestinian Authority does not yet constitute a state and is therefore not eligible to accede to the Rome Statute" that governs the ICC, the White House said.
"The United States continues to strongly oppose actions by both parties that undermine trust and encourages both sides to seek ways to deescalate tensions."
ICC membership allows the Palestinians to lodge war crimes complaints against Israel as of April.