The left-hander, who made 112 in the tour opener last week, smashed 86 as the Sri Lanka Cricket XI made 298-9 by stumps on the opening day of the three-day match at the Nondescripts Cricket Club here.
Strike bowler Steve Harmison added to England's worries when he left the field with back spasms after sending down the third ball of his 11th over an hour before close.
Harmison, a late entrant to the touring squad after proving his fitness playing first-class cricket in South Africa following hernia problems, finished the day with one for 45.
"Steve does not require scans, but is being treated and we will see how much he recovers overnight," England media manager Andrew Walpole told reporters.
Fast bowler Matthew Hoggard and left-arm spinner Monty Panesar claimed three wickets each.
Tharanga, who did not play on the recent Test tour of Australia, has been included in Sri Lanka's 14 for the first Test starting at the Asgiriya stadium in Kandy on Saturday.
The 22-year-old, with