The University of the Philippines (UP) and the De La Salle University (DLSU) slipped in the latest Times Higher Education (THE) World University Rankings.
UP slid down to 601-800 spot, from last year's 401-500 place, while DLSU fell to the 1,201+ from last year's 1,001+ spot.
The two are the only universities in the country to have made it to the list.
Ateneo de Manila University also appeared on the list but with a "reporter" status for failing to meet the eligibility criteria to receive a rank.
The United Kingdom's University of Oxford topped the rankings for the sixth consecutive year.
Over 1,600 universities across 99 countries and territories were included in this year's THE world university rankings.
Among the indicators used by THE to assess the schools are teaching, research, citations, international outlook, and industry income.