The intruder, aged around 35 years, had crossed the border and entered into Indian territory, sources said.
A BSF patrolling party challenged him but he did not stop, after which he was shot dead, the sources said.
"No objectionable object was found from the slain intruder," Rajendra Singh, Police Circle Officer of Anupgarh area said.
He said that senior police and BSF officers reached the spot and the BSF has also informed their counterpart in Pakistan about the incident.
"The body would be buried after post mortem if Pakistan rangers did not respond," Singh said.