Fox-Pitt, who claimed European bronze last week, found himself in fourth aboard Parklane Hawk with a score of 41.5 after the dressage and 22nd with Neuf des Coeurs.
It was with Neuf des Coeurs that the three-time Olympic medallist began the cross-country however they pulled up before fence 21 and were eliminated.
But there was to be no repeat with Parklane Hawk as, despite a 0.8 time penalty, Fox-Pitt maintained his position of fourth, even closing the gap on third.
Fox-Pitt sits level on 42.3 with Andrew Nicholson and Avebury having trailed the same rider and Nereo by 0.2 after the two days of dressage at Burghley.
New Zealander Nicholson is now fifth with Nereo and third with Avebury with compatriot Jock Paget occupying the top two positions going into the jumping.
Paget maintained his lead with Clifton Promise, their score after the cross-country 37.1, and jumped from fifth to second with Clifton Lush, they together are on 42.0
Of the other Brits at Burghley, Nicola Wilson ensured there is more than one in the top ten as she maintained ninth place with London 2012 Olympic ride Opposition Buzz.
Pippa Funnell is too still 13th while Kristina Cook fell from eighth to 14th and Sarah Cohen, the highest Brit after the first day of dressage, went from 17th to 20th.