Pradeep complained about stiffness in his hamstring after the second Test against Pakistan in Dubai, which the tourists won by 68 runs to complete a 2-0 series win.
Pradeep featured in both Tests and towards the end of the first Test was having trouble with his hamstring. Sri Lanka managed him well and he went onto share the new ball with Suranga Lakmal in the second Test.
He will undergo scans in Colombo to assess the seriousness of his injury. Fast bowler Lahiru Gamage, who made his Test debut in Dubai, has been retained for the ODIs.
The five-match ODI series gets underway in Dubai on Friday.