The soldier died Monday when the army moved against an attempt by the Movement of Democratic Forces of Casamance (MFDC) to install a new base near the border with The Gambia, and also destroy hemp fields, according to press reports.
Casamance, Senegal's southernmost region, is almost separated from the rest of the country by the tiny state of The Gambia, with a distinct culture and language stemming from its past as a Portuguese colony.
The MFDC has waged its campaign to break away since 1982 but signed a peace deal with the government last August, hailed as a first step toward a permanent end one of Africa's oldest active rebellions.
Officials also accuse the rebels of illicit trafficking of cannabis and wood, and of seeking refuge in The Gambia or in Guinea-Bissau to the south.
Senegal's President Macky Sall has said that ending the rebellion is a priority, and in recent years the government has begun returning Casamance residents displaced by the conflict.