The explosion apparently took place due to excessive pressure of the gases formed inside the toilet's septic tank in the city's Lokmanya Nagar locality last night, Thane Municipal Corporation's regional disaster management cell chief Santosh Kadam said.
The toilet seat was located on top of the septic tank which added to the pressure, he said.
The deceased was identified as Aakash Singh, a resident of Santosh Patil chawl, police said.
The boy's 55-year-old uncle who sustained injuries in the mishap was admitted to Thane Civil hospital.
Vartak Nagar police have registered a case of accidental death in this regard and were further probing, sub-inspector V R Patole said.