Khoja is a surname. Notable people with the surname include:
Abdulaziz bin Mohieddin Khoja (born 1940), Saudi Arabian diplomat
Afaq Khoja (date of birth unknown–1693/94), religious and political leader in Kashgaria (modern-day southern Xinjiang)
Ilyas Khoja (died 1368), Khan in Transoxiana and Khan of Moghulistan
Jahangir Khoja, a member of the influential East Turkestan Āfāqī khoja clan
Khaled Khoja (born 1965), Syrian Turkish politician
Muhammad Yusuf Khoja, 7th-century Naqshbandi Sufi figure
Khizr Khoja, son of the Chagatai khan Tughlugh Timur
Fictional characters
Warpriest Kh'oja, a fanatical and deceitful Skrull leader in Marvel Comics