"We call on President Rajapaksa to uphold Sri Lanka's commitments to security sector reform, accountability, respect for human rights and non-recurrence of violence," Pompeo said in a statement.
He called Sri Lanka a "valued partner" and voiced hope for cooperation in "fostering a free and open Indo-Pacific region where all countries can prosper" as well as on "deepening good governance and promoting justice, reconciliation and human rights."
Rajapaksa, who spearheaded the brutal finale of the Tamil Tiger conflict a decade ago, won a landslide win on the back of support from the majority Sinhalese Buddhist community.
He says he will no longer honor promises made by a previous government to the UN Human Rights Council at the behest of the United States to appoint an independent panel to look into alleged war crimes.
Sri Lankan troops are accused of killing up to 40,000 Tamil civilians in 2009 as they crushed the Tigers, who were notorious for suicide bombings in their decades-long insurgency. Both Rajapaksa and his brother Mahinda, who was president at the time, deny that the government killed civilians and accuse the Tigers of using civilians as human shields.
Weeks ahead of the election, Sri Lanka's outgoing leaders accepted a $480 million grant to improve infrastructure from the Millennium Challenge Cooperation, a US agency that rewards good governance.
China has aggressively courted Sri Lanka, including building an airport on the Rajapaksas' home turf that has no flights.
In 2017, Sri Lanka was forced to hand China a 99-year lease on a port after being unable to service a $1.4 billion Chinese loan, alarming Western and Indian officials who fear Beijing is pursuing a "string of pearls" strategy of creating hubs across the Indian Ocean.
Pompeo was set to visit Sri Lanka in June in the wake of Islamist attacks on Christian and Western sites that killed 269 people on Easter Sunday, but he abruptly canceled the stop.