The plural form of el pupitre is los pupitres.
In Spanish, to form the plural of nouns that end in a vowel, you typically add an -s to the end of the word. Since pupitre ends with a vowel (the letter -e), you simply add an -s, transforming el pupitre (the singular form) into los pupitres (the plural form). Remember that in Spanish, the definite article also changes from el (singular, masculine) to los (plural, masculine) when changing from singular to plural.