Egypt had protested on Wednesday a US decision to withhold some military and financial aid over human rights concerns.
In a phone call with Sisi, Trump "affirmed the strength of friendship between Egypt and the United States," the presidency said in a statement.
The US president said he was keen to continue "developing relations between the two countries and surpassing any obstacles that might affect them," according to the statement.
Trump's arrival in office in January has seen an improvement in US relations with Egypt, in contrast to his predecessor Barack Obama who took a harder line on human rights issues in the North African country.
Obama temporarily suspended military aid to Egypt after the July 2013 overthrow of Islamist president Mohamed Morsi and the subsequent bloody crackdown on Morsi's supporters.
Sisi in May approved a law which critics say will severely restrict the work of non-governmental organisations.
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