Mr Zelensky is said to have thanked Mr Johnson for his “decisive action” to help Ukraine following the Russian invasion.
Mr Johnson said there is “unwavering cross-party” support in the UK for Ukraine, and he pledged defensive aid would continue for as long as needed.
During his resignation speech outside Number 10 earlier on Thursday, Mr Johnson said the UK’s support for Ukraine is one of the key achievements of his premiership.
He most recently visited Kyiv last month.
The call between the two leaders took place on Thursday afternoon.
During his speech outside Downing Street, Mr Johnson said: “Let me say now, to the people of Ukraine, that I know that we in the UK will continue to back your fight for freedom for as long as it takes.”
The UK has provided weapons and training to Ukraine, with military and financial aid stepping up after the invasion began on February 24.
Earlier on Thursday, Defence Secretary Ben Wallace was asked if a change of leadership in the UK would affect the response to the war in Ukraine.
Speaking before the Prime Minister’s resignation statement, Mr Wallace said there was a cross-party consensus on Ukraine.
He said President Zelensky and Defence Minister Oleksii Reznikov both knew the UK is “full-square behind them”.