Police discovered a first casualty at around 1am, who was pronounced dead at the scene after sustaining serious injuries consistent with electrocution.
At 2.30am, officers were then called to a reports of a second casualty, further along the line closer to Stratford.
The individual was also declared dead from suspected electrocution.
BTP officers remained on the scene on Thursday morning, where they were trying to establish how the two casualties came to be on the tracks a significant distance away from each other.
Enquiries are also underway to identify the deceased and inform their families.
“An investigation is now underway to discover what happened and how these two people came to lose their lives on the railway,” said DCI Tim Tubbs of the BTP.
“At this time we are treating their deaths as unexplained as we make a number of urgent enquiries.
“I would ask anyone who was near Stratford or Hackney Wick last night, and saw something which they think might be relevant to contact us as soon as possible.”
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