diff --git a/lib/commands/instrument.js b/lib/commands/instrument.js
index fc490890d..9e255a757 100644
--- a/lib/commands/instrument.js
+++ b/lib/commands/instrument.js
@@ -1,4 +1,6 @@
 const NYC = require('../../index.js')
+const path = require('path')
+const rimraf = require('rimraf')
 
 exports.command = 'instrument <input> [output]'
 
@@ -51,6 +53,11 @@ exports.builder = function (yargs) {
       type: 'boolean',
       description: 'tell the instrumenter to treat files as ES Modules'
     })
+    .option('delete', {
+      describe: 'should the output folder be deleted before instrumenting files?',
+      default: false,
+      type: 'boolean'
+    })
     .example('$0 instrument ./lib ./output', 'instrument all .js files in ./lib with coverage and output in ./output')
 }
 
@@ -72,6 +79,16 @@ exports.handler = function (argv) {
     exitOnError: argv.exitOnError
   })
 
+  if (argv.delete && argv.output && argv.output.length !== 0) {
+    const relPath = path.relative(process.cwd(), path.resolve(argv.output))
+    if (relPath !== '' && !relPath.startsWith('..')) {
+      rimraf.sync(argv.output)
+    } else {
+      console.error(`nyc instrument failed: attempt to delete '${process.cwd()}'`)
+      process.exit(1)
+    }
+  }
+
   nyc.instrumentAllFiles(argv.input, argv.output, function (err) {
     if (err) {
       console.error(err.message)
diff --git a/test/nyc-integration.js b/test/nyc-integration.js
index 0eba6aaa5..a34bbdbc8 100644
--- a/test/nyc-integration.js
+++ b/test/nyc-integration.js
@@ -11,6 +11,7 @@ const fs = require('fs')
 const glob = require('glob')
 const isWindows = require('is-windows')()
 const rimraf = require('rimraf')
+const makeDir = require('make-dir')
 const spawn = require('child_process').spawn
 const si = require('strip-indent')
 
@@ -622,6 +623,10 @@ describe('the nyc cli', function () {
     })
 
     describe('output folder specified', function () {
+      afterEach(function () {
+        rimraf.sync(path.resolve(fixturesCLI, 'output'))
+      })
+
       it('allows a single file to be instrumented', function (done) {
         var args = [bin, 'instrument', './half-covered.js', './output']
 
@@ -635,7 +640,6 @@ describe('the nyc cli', function () {
           var files = fs.readdirSync(path.resolve(fixturesCLI, './output'))
           files.length.should.equal(1)
           files.should.include('half-covered.js')
-          rimraf.sync(path.resolve(fixturesCLI, 'output'))
           done()
         })
       })
@@ -653,7 +657,6 @@ describe('the nyc cli', function () {
           var files = fs.readdirSync(path.resolve(fixturesCLI, './output'))
           files.should.include('env.js')
           files.should.include('es6.js')
-          rimraf.sync(path.resolve(fixturesCLI, 'output'))
           done()
         })
       })
@@ -670,7 +673,6 @@ describe('the nyc cli', function () {
           code.should.equal(0)
           var files = fs.readdirSync(path.resolve(fixturesCLI, './output'))
           files.should.include('index.js')
-          rimraf.sync(path.resolve(fixturesCLI, 'output'))
           done()
         })
       })
@@ -721,6 +723,88 @@ describe('the nyc cli', function () {
           })
         })
       })
+
+      describe('delete', function () {
+        beforeEach(function () {
+          makeDir.sync(path.resolve(fixturesCLI, 'output', 'removed-by-clean'))
+        })
+
+        it('cleans the output directory if `--delete` is specified', function (done) {
+          const args = [bin, 'instrument', '--delete', 'true', './', './output']
+
+          const proc = spawn(process.execPath, args, {
+            cwd: fixturesCLI,
+            env: env
+          })
+
+          proc.on('close', function (code) {
+            code.should.equal(0)
+            const subdirExists = fs.existsSync(path.resolve(fixturesCLI, './output/subdir/input-dir'))
+            subdirExists.should.equal(true)
+            const files = fs.readdirSync(path.resolve(fixturesCLI, './output'))
+            files.should.not.include('removed-by-clean')
+            done()
+          })
+        })
+
+        it('does not clean the output directory by default', function (done) {
+          const args = [bin, 'instrument', './', './output']
+
+          const proc = spawn(process.execPath, args, {
+            cwd: fixturesCLI,
+            env: env
+          })
+
+          proc.on('close', function (code) {
+            code.should.equal(0)
+            const subdirExists = fs.existsSync(path.resolve(fixturesCLI, './output/subdir/input-dir'))
+            subdirExists.should.equal(true)
+            const files = fs.readdirSync(path.resolve(fixturesCLI, './output'))
+            files.should.include('removed-by-clean')
+            done()
+          })
+        })
+
+        it('aborts if trying to clean process.cwd()', function (done) {
+          const args = [bin, 'instrument', '--delete', './', './']
+
+          const proc = spawn(process.execPath, args, {
+            cwd: fixturesCLI,
+            env: env
+          })
+
+          let stderr = ''
+          proc.stderr.on('data', function (chunk) {
+            stderr += chunk
+          })
+
+          proc.on('close', function (code) {
+            code.should.equal(1)
+            stderr.should.include('nyc instrument failed: attempt to delete')
+            done()
+          })
+        })
+
+        it('aborts if trying to clean outside working directory', function (done) {
+          const args = [bin, 'instrument', '--delete', './', '../']
+
+          const proc = spawn(process.execPath, args, {
+            cwd: fixturesCLI,
+            env: env
+          })
+
+          let stderr = ''
+          proc.stderr.on('data', function (chunk) {
+            stderr += chunk
+          })
+
+          proc.on('close', function (code) {
+            code.should.equal(1)
+            stderr.should.include('nyc instrument failed: attempt to delete')
+            done()
+          })
+        })
+      })
     })
   })