Koizumi left Pakistan on Sunday for Luxembourg ahead of talks with EU leaders on Monday in which he was expected to reiterate Japan's opposition to proposals to lift the bloc's arms embargo on China.
During his visit, Koizumi held wide-ranging talks with President Pervez Musharraf on Saturday, conveying Tokyo's concern over nuclear proliferation after revelations about an illegal nuclear network run by Pakistan's top scientist Abd al-Qadir Khan.
Musharraf assured him Pakistan's nuclear assets were in safe hands.
The yen loans for Pakistan, amounting to hundreds of millions of dollars, were suspended by Tokyo in 1998 after Pakistan conducted nuclear tests.
Koizumi said the resumption of new loans, amounting to around $160 million, was meant to strengthen ties with Pakistan.
The Japanese prime minister earlier visited Pakistan's neighbour and rival India, where he also reached agreements to boost ties with the growing economic and geo-political power while both countries renewed support for each other's bids for UN Security Council seats.