Darlene Phillips, the boy's maternal grandmother and primary caregiver, was arrested Friday night and remained in the Collin County Detention Facility in McKinney on Saturday.
Her bail was set at $500,000.
Wylie investigators confirmed the identity of the boy late Friday as Gerren Joseph Isgrigg. His body was found April 15 near a Collin County lake. Police think the body was abandoned less than 24 hours before it was found.
Police have said he was small for his age, weighing just 28 pounds, and had "significant medical needs." He showed signs of having had a feeding tube.
"Gerren was not taken care of well," Wylie Detective Venece Perepiczka told The Dallas Morning News, adding that the boy was not physically able to care for himself.
Autopsy results are pending, but police have said there were no obvious injuries.
Police have not said where the 63-year-old Phillips lived. Police said the boy's parents are separated, with his father living in California and his mother living in Oklahoma. The names of the parents were not released.
Police said a tip to the National Center for Missing and Exploited Children's hotline led to Gerren's identification.
The discovery of his body had touched many, with a candlelight vigil Thursday bringing hundreds of people to a Wylie park to pray for answers to his identity.
A "Wylie's Angel" Facebook page has seen membership grow to 44,000.