The US delegation included treasury and commerce representatives, as well as officials from the US state of Florida.
Representatives of various Cuban ministries and state companies were taking part in the talks, which the foreign ministry has said would be centered on recent US steps to ease trade and other restrictions with the communist-ruled country.
"We can build a more open relationship between our two nations," said Pritzker.
The United States and Cuba restored diplomatic relations in July after a 54-year break that outlasted the Cold War and froze trade between the two countries.
US President Barack Obama in September lifted a cap on remittances by US-based Cubans, and authorized joint ventures with Cuban state companies and tourist visits to the island on American cruise ships and airlines.
But an overarching US trade embargo remains in effect, with little prospect of being lifted by the Republican-controlled US Congress.
Cuba's minister of foreign trade and foreign investment, Rodrigo Malmierca, told the US delegation Havana appreciates "the measures President Obama has taken in the sense of giving flexibility to the reach of the blockade" of the island.
But other restrictions that remain in effect, like a ban on Cuba using the dollar as a payment currency, have complicated implementation of the measures taken by Obama.
Those issues were expected to come up in the Havana talks.
Pritzker, who arrived in Cuba Tuesday, visited the Mariel megaport and free trade zone, where she said she wanted to better understand how each side works to find ways to advance the relationship, according to local press reports.
The Mariel megaport is a centerpiece of President Raul Castro's efforts to attract foreign investment to Cuba and develop it into a regional distribution hub.
Trade between the two countries amounted to only $390 million in 2014, down from $598 million in 2009, according to official Cuban statistics.
Cuba is barred from exporting goods to the United States and has only been able to import food and medicine from its northern neighbor since 2001.
Under current rules, US imports by Cuba must be paid in advance through complicated bank transactions and can only be shipped on vessels authorized by the United States.