Riding Sugoi in the FEI World Cup Eventing class, Tompkins jumped clear but added 2.8 time penalties to her dressage score.
Tompkins can afford to drop two rails in tomorrow's show jumping phase.
Anne-Marie Styles on Opera Groove also jumped clear on the cross country but added 8 time penalties and retain second position overnight. Last year's winner Clarke Johnstone had a run-out at the stump before the second water, to drop from third position to seventh.
Jonathan Pagent on the relatively inexperienced Clifton Promise were the trail blazers on the cross country and move into third position. The event concludes tomorrow with the show jumping.