Houghton opened the scoring in England’s controversial 3-0 last-16 triumph over Cameroon in Valenciennes on Sunday with new City colleague Ellen White also on target for her fourth goal of the tournament.
But after producing a player of the match display, Houghton was then the victim of an injury time late tackle by Alexandra Takounda in a match marred by twin VAR protests from the Cameroon players and a series of other controversial incidents.
Though Houghton was able to return to pitch, Neville later revealed there were worries over the fitness of his skipper.
“Steph Houghton was player of the match and can't be here as she's on the treatment table, from the tackle that everyone saw,” Neville said in his post-match press conference.
“She needs to recover, she’s in a lot of pain.
"We're concerned about her, she's not someone that stays down.
“It was a late tackle and we're going to have to do everything possible to get her fit for the quarter-final. She's a big player for us, our captain.”
In spite of the protests from the Cameroon players and Houghton’s subsequent injury, there were numerous positives for England, with Alex Greenwood’s late second half strike rounding off the win.
White’s goal set the seal on another fine individual display while her City colleague Jill Scott marked her 18th World Cup appearance – a record for any England player – with another assured display.
Sunday’s other last-16 game was equally dramatic and again dominated by VAR decisions with hosts France overcoming Brazil 2-1 thanks to an extra time strike from Amandine Henry.
Valerie Gauvin, who had earlier had a goal ruled out by VAR, put France ahead after a fine run by Kadidiatou Diani.
Brazil forced extra-time when Thaisa's drive, originally ruled out for offside, was subsequently awarded after another VAR check in Le Havre.
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With the prospect of a penalty shoot-out looming, Amandine Henry got on the end of Amel Majri's long free-kick for the winner.
France’s reward is a quarter-final tie against either the United States or Spain who face a last 16 clash today in Reims, kick-off 5.30pm.
That’s followed at 8pm by an eagerly-awaited game between Janine Beckie’s Canada and Sweden who meet in Paris.