The two nations have been working together since 2006 to develop a variant of the Standard Missile-3, a ship-launched missile that operates as part of the Aegis Ballistic Missile Defense System.
Tuesday evening's test saw a medium-range ballistic target launched from the Pacific Missile Range Facility at Kauai, Hawaii, the US Missile Defense Agency said in a statement.
The USS John Paul Jones guided-missile destroyer detected and tracked the target missile with its onboard radar using Aegis.
"Upon acquiring and tracking the target, the ship launched an SM-3 Block IIA guided missile, but the missile did not intercept the target," the MDA said.
This was the fourth development flight test using an SM-3 IIA missile, and the second such intercept test.
The previous test, in February 2017, was successful.
According to the MDA, America has so far spent about $2.2 billion on the system and Japan about $1 billion.
The test comes amid heightened tensions around North Korea's continued advances in its ballistic missile program.
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