Obama arrived Friday for a three-day visit of regional meetings, his second trip there since April last year.
Muslim men wearing skull caps and women in colorful headscarves rallied Saturday near a Kuala Lumpur convention center, where Obama is due to meet Southeast Asian leaders later Saturday, AP reported.
They chanted "Reject Obama" and held banners that read "O Terrorist, you are not welcome here."
Ten Southeast Asian heads of state and nine world leaders, including President Barack Obama, are meeting in Malaysia to discuss trade and economic issues. Terrorism and disputes over the South China Sea are also on the agenda.