Boncourt has an area of 9.02 km² (3.48 sq mi).
 Of this area, 3.74 km² (1.44 sq mi) or 41.5% is used for agricultural purposes, while 3.42 km² (1.32 sq mi) or 38.0% is forested.
  Of the rest of the land, 1.81 km² (0.70 sq mi) or 20.1% is settled (buildings or roads), 0.05 km² (12 acres) or 0.6% is either rivers or lakes.

Of the built up area, housing and buildings made up 9.3% and transportation infrastructure made up 3.7%.
 Power and water infrastructure as well as other special developed areas made up 5.1% of the area  Out of the forested land, 36.7% of the total land area is heavily forested and 1.2% is covered with orchards or small clusters of trees.
 Of the agricultural land, 20.8% is used for growing crops and  15.8% is pastures, while 2.2% is used for orchards or vine crops and 2.8% is used for alpine pastures.
 All the water in the municipality is flowing water.

The municipality is located in the Porrentruy district, on the border with France.
 The large industrial village is the most important border crossing between the Canton of Jura and France.
Boncourt has an area of 9.02 km² (3.48 sq mi).  Of this area, 3.74 km² (1.44 sq mi) or 41.5% is used for agricultural purposes, while 3.42 km² (1.32 sq mi) or 38.0% is forested.   Of the rest of the land, 1.81 km² (0.70 sq mi) or 20.1% is settled (buildings or roads), 0.05 km² (12 acres) or 0.6% is either rivers or lakes.
Of the built up area, housing and buildings made up 9.3% and transportation infrastructure made up 3.7%.  Power and water infrastructure as well as other special developed areas made up 5.1% of the area  Out of the forested land, 36.7% of the total land area is heavily forested and 1.2% is covered with orchards or small clusters of trees.  Of the agricultural land, 20.8% is used for growing crops and  15.8% is pastures, while 2.2% is used for orchards or vine crops and 2.8% is used for alpine pastures.  All the water in the municipality is flowing water.
The municipality is located in the Porrentruy district, on the border with France.  The large industrial village is the most important border crossing between the Canton of Jura and France.
Boncourt, Switzerland