Toon legend Srnicek died of a heart attack in 2015 aged 47.
The ex-Czech Republic keeper played 190 times over two spells at St James' Park between 1991 and 2007.
Supporters honoured him with a flag reading "Pavel is a Geordie" which is displayed at games.
After it went missing following Newcastle's 2-1 home loss to Chelsea, Magpies academy coach Harper tweeted: "Could whoever has taken the 'Pavel is a Geordie' flag please return it ASAP.
"The big man meant so much to so many people and it's only fitting he's remembered whenever NUFC play."
Newcastle will look at CCTV footage today in an attempt to find the culprit.
Srnicek, who was capped 49 times, helped Newcastle gain promotion to the Premier League in the 1992-93 season under Kevin Keegan.
He was an important part of the squad that nearly won the Prem three years later, rotating with Shaka Hislop.
Newcastle fans tweeted their disgust that his flag had been stolen.
One wrote: "Why on fe**in earth would anyone think stealing I flag in memory is beyond belief !!!"
Another said: "It's an absolute disgrace….sort this out now."
Meanwhile, pranksters have apologised for hacking DeAndre Yedlin's Instagram account and threatening to post his private messages.
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