Susan Tanner, 37, explained that she had caught the Number 102 bus with her youngest son, Tommy, and his six-year-old brother, Frankie, from their home in New Romney, Kent.
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But, despite paying the £6.40 fare, the family were kicked off the bus when her 15-month-old began to cry.
The furious mother told the Mail Online: "The driver said 'Do you need some time out?' I asked what he meant.
"He then said 'Do you need to get off the bus because the baby is crying?'
"I said no, and I asked the other passengers if the baby was disturbing them. None of them said so.
"The driver then said 'It's disturbing me and I would like you to get off the bus'."
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She added: "I am still in shock. I couldn't believe it."
A Stagecoach spokesman said the driver's action was strongly against company policy.
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He said: 'We were very concerned to hear about this incident.
"We have carried out an investigation to find out what happened and can confirm that one of our drivers suggested Ms Tanner alight the bus.
"This is definitely not part of any company procedure or policy and we would like to offer Miss Tanner our sincere apologies for our driver's actions.
"We will take appropriate action to prevent this from ever happening again."