Although the 18-month-old's wound had now healed, the family was scared to return home, his father said.
Satrin Osinya was wounded when unknown gunmen opened fire on a church near the coastal city of Mombasa on 23 March.
Six people died in the attack, including Satrin's mother, who was buried last week.
Doctors believe the bullet which killed her while she was shielding her son exited her body and buried itself in his head during the shooting.
'Playing with toys'The bullet was removed about a week later during a three-hour operation at the Kenyatta National Hospital in the capital, Nairobi.
Bibles covered in blood lay on the church's floor after the shooting A photo of Satrin Osinya held by his older brother after the attack - and the X-ray showing the bulletBenson Osinya said he was thankful his son had recovered, but "there's a gap in my life because I have no wife".
The toddler and his elder brother Moses were too afraid to return to Mombasa, he added.
Satrin was seen flashing a radiant smile and rolling his toys at the hospital on Wednesday, a day before he was discharged, Kenya's privately owned Standard newspaper reported.
He was flown from Mombasa to Nairobi for the operation soon after the shooting.
Kenyan police say the attack on the church could have been an "act of terrorism".
At least two gunmen burst into the building and started shooting indiscriminately.
The attackers managed to escape on foot before the police arrived.
Blood-soaked Bibles and overturned chairs lay strewn across the church's floor after the shooting.
There have been several incidents of violence in Mombasa in recent months, involving the security forces and Islamist militants.
However, no group has said it carried out the attack.