The 16-month-old tot reportedly stopped sleeping properly and cries when she is put on her back.
According to a report in Britain's The Sun newspaper, Brad wants to take Zahara to the US for treatment but heavily-pregnant Angelina wants to stay in Africa until she delivers her baby.
A source said: "Brad is absolutely beside himself. He's desperate to take Zahara to the US for medical attention. But Angie insists on staying in Africa.
"It has caused a number of fights between them."
It's thought Zahara may have a genetic illness, but a number of tests have failed to provide any clues.
The source added: "She's had so many tests, but no one knows what is wrong."
Brad and Angelina, who also has an adopted son, four-year-old Maddox, have reportedly sold the first picture of their unborn baby for a staggering £2.6million.
The pair allegedly negotiated the huge fee, which will be donated to charity, with an American weekly magazine.

Meanwhile, reports claim that Brad Pitt is still calling ex-wife Jennifer Aniston and that has the very pregnant Angelina Jolie in tears.

Even Close to Birth, Angie Worries About Brad and Jen

The story details that all is not well with the couple as Jolie is near birth and she is stressed that Brad is still in contact with Jennifer reports ChinaDaily

"Angelina and Brad have been fighting constantly for the past several months," revealed an insider. "And she was especially livid when she found out that he had made secret phone calls to Jennifer regarding a movie project," the report reads.

Copyright Bang Media + Agencies