The firm said in a statement profits for the quarter were up 12 percent and that the job cuts were part of a $300 million restructuring programme to strengthen productivity.
Sales in the July through September period increased by 18 percent to $14.84 billion.
Novartis said it would begin consulting with employees on the modalities of the job cuts. The company said it would create 700 new jobs, mainly in countries with a lower cost base.
The cost-saving measures are to be spread over three to five years, the company said. In the plan, Novartis expects to close one plant in Switzerland and another in Italy.
Research currently based in Switzerland would be transferred to the United States, Novartis said
After the earnings news, shares in Novartis fell by 0.97 percent on Tuesday morning, in a Zurich market down by 0.30 percent.