Amy Bate said her two-year-old son Oscar found the needle under a table at the Glass House in St Helens on Sunday (21 October).
Oscar was taken to hospital for a blood test and given a hepatitis vaccination in his leg. He will need several months of hospital checks, including blood tests every three months after a period of further treatment.
Bate told the regional newspaper the Liverpool Echo she had felt distressed ever since she realised the needle pricked her toddler.
She said: “My son climbed under the table and picked up something that looked like a dark blue marker pen lid and I told him to put it down and that it was dirty.
“I felt sick literally as soon as I realised he had been pricked by it and knew we had to take him the hospital straight away as my first thought was oh my god, what if he's got HIV?”
The pubco confirmed to The Morning Advertiser that the pub would carry out its own investigation into how the incident happened.
A spokesperson for JD Wetherspoon added that the pub manager had apologised to the family.
JD Wetherspoon spokesman Eddie Gershon said: “The manager at the pub and the company apologise wholeheartedly to the lady and her family.
“This is a horrible incident and obviously shouldn’t happen.
“The lady and her child shouldn’t have had to go through the trauma of having an HIV test at the hospital.”
Gershon added: “The manager at the pub would like to offer the lady a £50 gift card for use at the pub.
“This in no way underestimates the situation that she faced.”
There have not been any recorded cases of discarded needles leading to HIV infections, according to the National Aids Trust charity.
Infections that used needles can pass on to other people include hepatitis B, hepatitis C and HIV.