She detailed her “concerns” in a letter to the sport’s governing body this week.
“To have the opportunity to compete for Great Britain in Australia is a privilege,” she wrote.
“When I started running, the prospect of me competing in the World Cross Country Championships would have seemed merely a dream. However, the reality of the travel fills me with deep concern.
“I was just nine when the COP21 Paris Climate agreement was signed. Now, eight years on, and global emissions have been steadily increasing, sending us on a path to climate catastrophe.”
The 16-year-old added she would “never be comfortable” flying and that it would cause her grief.
“Coming to a decision has not been easy, however little compares to the grief I would feel taking the flight.”
In December, the 16-year-old dominated the European Cross Country Championships in Turin.
Read Related Also: Gisele Bündchen’s gorgeous green beaded bikini is 50% off
She set a national under-17 record for 3000-metres, and finished fourth in the 4000-metre race at the under-20s, going against athletes three years older.
The wins came despite the fact she missed much of her preparation because she was travelling.
Her 20-hour journey to the northern Italian city involved coaches, trains and cycling from station to station.
What sea level rise will look like around the globe
FitzGerald has previously ruled herself out of competing at the European Under-18 Championships in Jerusalem.
Her concerns about travelling via aircraft stem from flight emissions; the aviation sector currently accounts for two per cent of emissions globally.
According to the International Civil Aviation Organisation (ICAO), one person flying from London to Sydney via Singapore would be responsible for 1.74 tonnes of CO2.