The President was accorded a warm red carpet welcome on his arrival at the Naypyidaw International Airport as he alighted from his plane.
Myanmar's Union Minister for Health Dr Pe Thet Khin and Union Minister for Education Dr Mya Aye, Pakistan ambassador to Myanmar and high ranking officials received the President and his delegation.
Later, President Zardari and his entourage drove off for President House where he will hold a meeting with the President of Myanmar Thein Sein.
The two leaders will exchange views on bilateral, regional and international issues of mutual interest.
They will discuss ways to expand cooperation in multifaceted fields especially focusing on steps to achieve closer regional economic integration.
They will be keen to increase mutual cooperation in a number of areas and would be looking to firm up proposals for increased high level contacts and frequent exchange of business and trade delegations of the two countries.
On Wednesday, the President will travel to Yangon to meet with icon of democracy and head of National League for Democracy (NLD) Aung San Suu Kyi at her residence.
President Zardari will confer Mohtarma Benazir Bhutto Shaheed Award on Aung San Suu Kyi in a special investiture ceremony. Suu Kyi was awarded the Nobel Peace Prize in 1991 and she is known worldwide for her decades long struggle for the democracy.
Later, the President will pay a visit to the mausoleum of last Mughal emperor Bahadur Shah Zafar.
Pakistan and Myanmar enjoy cordial ties going back to 1948, when Myanmar achieved independence from Britain.
President Zardari has been keenly pursuing ties with neighbours of Pakistan and regional countries, undertaking numerous visits to China, which is neighbor of Myanmar.
Myanmar, which is rich in natural resources, has undertaken joint development projects with many neighbouring countries including China.
Pakistan is actively working to sign a Free Trade Agreement (FTA) with Association of South East Asian Nations (ASEAN), an influential regional bloc. Myanmar is an important member of ASEAN, which includes countries likeIndonesia, Malaysia, Singapore and Thailand.