This comes after the departure board had featured an Islamic "Hadith of the day" which called on "sinners to repent."
The hadith is a compilation of the words and deeds of the Islamic prophet Muhammad.
People began to complain on social media after pictures were posted of the messaging board.
Humanists UK posted a statement on X saying it felt public train stations "should not be urging 'sinners' to repent".
The campaign group said: "It is obviously inappropriate and profoundly misjudged to broadcast hadiths or any religious scripture at passengers. We will be writing to the transport secretary to outline our concerns."
"We welcome Network Rail's decision to remove hadiths from the departure board at King's Cross," said NSS chief executive Stephan Evans in a statement on the organization's website.
"At best this was a well-meaning yet misguided and counterproductive attempt at inclusivity," he said.
Multiple photographs circulated on social media which showed the departure board displaying Islamic prayer times and hadiths.
One photo showed a hadith that read: "The Prophet Muhammad (PBUH) said: All the sons of Adam are sinners but the best of the sinners are those who repent often."
Another hadith featured in an additional photo read: "The gates of Hellfire are closed, and the devils are chained."
While Evans insisted that the British people are welcoming of all different religions, the organization felt that the display board opened the door to other religions wanting equal recognition and that it had been forcing Islam on people who might not share the same beliefs.
"British people tend to be comfortable with diversity and people being free to practise their religion. What they're not so keen on is other people's religion being imposed on them. I don't think they want to be told they're sinners when they're catching a train," said Evans.
"Such gestures also risk accusations of favouritism, generating resentment and the inevitable demands from other religious or identity groups for equal recognition," he added. "Maintaining religious neutrality in public spaces and services is the best way of nurturing a harmonious, even-handed and inclusive society that respects all individuals, regardless of their beliefs or backgrounds."
The hadith, according to Network Rail, were shown in observance of the Islamic month of Ramadan, which falls this year between March 10 and April 9.
A spokesperson for Network Rail said: "We value the feedback of our passengers and while these messages were intended to celebrate the beliefs and backgrounds of some of our colleagues and passengers, we have removed them."
