Authorities say in both cases the attackers hurled grenades and opened fire on worshippers.
The deadliest attack took place at the African Inland Church, where at least 10 people were killed, including two police officers. The second attack took place at a Catholic church.
Garissa is located about 140 kilometers west of the Somalia border. It is also about 80 kilometers southwest of the sprawling Dadaab refugee camp, which houses nearly 500,000 Somali refugees.
On Friday, several gunmen at the Dadaab camp killed one Kenyan and kidnapped four foreign aid workers.
Kenyan sent troops into Somalia last year to pursue al-Shabab militants. Since then, Kenya has blamed the al-Qaida-allied group for a series of attacks and kidnappings on Kenyan soil.
Al-Shabab says it is trying to overthrow U.N.-backed transitional government and impose a strict form of Sharia law throughout Somalia. VoA.