The Crystal Palace full-back was targeted by away fans during Saturday's FA Cup fifth round tie.
Chilwell, who is on loan from Chelsea, played the full 90 minutes for Oliver Glasner's side.
During the match, shouts of 'Chelsea rent boy' were aimed at Chilwell by the travelling supporters.
The FA are said to be investigating the homophobic chants.
However, chants aimed at Jean-Philippe Mateta whilst he received treatment will not be probed.
READ MORE IN FOOTBALL
Mateta conscious in hospital with serious ear injury after shocking Millwall challenge
'Most reckless challenge I've ever seen' - Palace chief rages after Mateta hospitalised
Chants of 'let him die' were heard from the away end as Mateta lay prone on the turf after receiving a boot to the face from Millwall goalkeeper Liam Roberts.
But it is understood those chants do not breach FA regulations.
Mateta was stretchered off and taken to hospital after a flying kick from Roberts, which earned the Millwall goalkeeper a straight red card following a VAR review.
Meanwhile, Palace chairman Steve Parish described it as "the most reckless challenge on a football pitch that I think I've ever seen".
Most read in Football
'This is an absolute disgrace' - VAR chaos at Bournemouth leaves broadcasters furious
Frank Lampard achieves 39-year feat as Coventry move into Championship play-offs
'Most reckless challenge I've ever seen' - Palace chief rages after Mateta hospitalised
Revolutionary new football rule approved and it will start from next season
The hosts went on to take the lead through a Japhet Tanganga own goal before Daniel Munoz doubled their advantage.
Wes Harding pulled one back during first half stoppage-time before a late Eddie Nketiah strike secured Palace's place in the last eight.
The Premier League side join Aston Villa and Preston in Sunday's quarter-final draw.
It is Palace's best run in the competition since reaching the semi-finals three years ago.
As for Chilwell, he has now made four appearances since signing for the club on deadline day.
After completing his first 90 minutes for Palace, the defender told talkSPORT: "For the past six months, I've been doing it for myself, training every day. Some days I've been training by myself.
"So, yeah, not here, but Chelsea, I've been training by myself some of the days. And it's just like I said, doing it for myself.
"I knew this day was going to come and it was down to me to make sure that I was ready. And you can't feel sorry for yourself.
"You've just got to put the work in and, you know, your chance is going to come. And the only person that's going to miss out if you're not ready is yourself.
"So that's been my mindset the past however many months. And like I said, again, I've come in to help the squad.
"It's an ambitious team that wants to do well. Again, like I said, and personally, I want to do well and get back to showing everyone that I'm a top world class left back, left wing back, whatever you want to call it.
"Personally, I feel like I've got stuff to prove. You feel like when you're out of the game for a few months, people forget about you.
Read More on talkSPORT
Sir Chris Hoy shares heart-rending cancer update that left him with broken spine
Floyd Mayweather poses with most expensive ever purchase worth $402million
"I think personally my ego, everyone has an ego in football and I'm not going to shy away from it.
"You know, I want to show everyone that I am as good as what I was when I won the Champions League."
That's really dangerous' - Jean-Philippe Mateta rushed to hospital after horrible Millwall challenge