diff --git a/centipede/batch_fuzz_example/customized_centipede_test.sh b/centipede/batch_fuzz_example/customized_centipede_test.sh
index 4d3e206..40fe788 100755
--- a/centipede/batch_fuzz_example/customized_centipede_test.sh
+++ b/centipede/batch_fuzz_example/customized_centipede_test.sh
@@ -63,9 +63,9 @@
 fuzztest::internal::test_replaying_target \
   batch_fuzz 'RSS limit exceeded: [0-9][0-9]* > 1024' "oom"
 
-export CENTIPEDE_RUNNER_FLAGS=":timeout_per_input=1:"
+export CENTIPEDE_RUNNER_FLAGS=":timeout_per_input_ms=1000:"
 echo -e "\n=== Timeout test with CENTIPEDE_RUNNER_FLAGS=${CENTIPEDE_RUNNER_FLAGS}\n"
 fuzztest::internal::test_replaying_target \
-  batch_fuzz 'Per-input timeout exceeded: [0-9][0-9]* > 1' "slp"
+  batch_fuzz 'Per-input timeout exceeded: [0-9][0-9]* > 1000' "slp"
 
 echo "PASS"
diff --git a/centipede/centipede_callbacks.cc b/centipede/centipede_callbacks.cc
index 819e800..4eb484d 100644
--- a/centipede/centipede_callbacks.cc
+++ b/centipede/centipede_callbacks.cc
@@ -112,8 +112,8 @@
     std::string_view extra_flags, bool disable_coverage) {
   std::vector<std::string> flags = {
       "CENTIPEDE_RUNNER_FLAGS=",
-      absl::StrCat("timeout_per_input=", env_.timeout_per_input),
-      absl::StrCat("timeout_per_batch=", env_.timeout_per_batch),
+      absl::StrCat("timeout_per_input_ms=", env_.timeout_per_input * 1000),
+      absl::StrCat("timeout_per_batch_ms=", env_.timeout_per_batch * 1000),
       absl::StrCat("address_space_limit_mb=", env_.address_space_limit_mb),
       absl::StrCat("rss_limit_mb=", env_.rss_limit_mb),
       absl::StrCat("stack_limit_kb=", env_.stack_limit_kb),
diff --git a/centipede/runner.cc b/centipede/runner.cc
index d998350..e6223d8 100644
--- a/centipede/runner.cc
+++ b/centipede/runner.cc
@@ -185,7 +185,7 @@
 }
 
 static void CheckWatchdogLimits() {
-  const uint64_t curr_time = time(nullptr);
+  const uint64_t curr_time_ms = TimeInUsec() / 1000;
   struct Resource {
     const char *what;
     const char *units;
@@ -194,23 +194,23 @@
     bool ignore_report;
     const char *failure;
   };
-  const uint64_t input_start_time = state.input_start_time;
-  const uint64_t batch_start_time = state.batch_start_time;
-  if (input_start_time == 0 || batch_start_time == 0) return;
+  const uint64_t input_start_time_ms = state.input_start_time_ms;
+  const uint64_t batch_start_time_ms = state.batch_start_time_ms;
+  if (input_start_time_ms == 0 || batch_start_time_ms == 0) return;
   const Resource resources[] = {
       {Resource{
           /*what=*/"Per-input timeout",
-          /*units=*/"sec",
-          /*value=*/curr_time - input_start_time,
-          /*limit=*/state.run_time_flags.timeout_per_input,
+          /*units=*/"ms",
+          /*value=*/curr_time_ms - input_start_time_ms,
+          /*limit=*/state.run_time_flags.timeout_per_input_ms,
           /*ignore_report=*/state.run_time_flags.ignore_timeout_reports != 0,
           /*failure=*/kExecutionFailurePerInputTimeout.data(),
       }},
       {Resource{
           /*what=*/"Per-batch timeout",
-          /*units=*/"sec",
-          /*value=*/curr_time - batch_start_time,
-          /*limit=*/state.run_time_flags.timeout_per_batch,
+          /*units=*/"ms",
+          /*value=*/curr_time_ms - batch_start_time_ms,
+          /*limit=*/state.run_time_flags.timeout_per_batch_ms,
           /*ignore_report=*/state.run_time_flags.ignore_timeout_reports != 0,
           /*failure=*/kExecutionFailurePerBatchTimeout.data(),
       }},
@@ -270,7 +270,7 @@
     sleep(1);
 
     // No calls to ResetInputTimer() yet: input execution hasn't started.
-    if (state.input_start_time == 0) continue;
+    if (state.input_start_time_ms == 0) continue;
 
     CheckWatchdogLimits();
   }
@@ -282,7 +282,7 @@
   // Check for the stack limit only if sp is inside the stack region.
   if (stack_limit > 0 && tls.stack_region_low &&
       tls.top_frame_sp - sp > stack_limit) {
-    const bool test_not_running = state.input_start_time == 0;
+    const bool test_not_running = state.input_start_time_ms == 0;
     if (test_not_running) return;
     if (stack_limit_exceeded.test_and_set()) return;
     fprintf(stderr,
@@ -308,11 +308,11 @@
 
 void GlobalRunnerState::StartWatchdogThread() {
   fprintf(stderr,
-          "Starting watchdog thread: timeout_per_input: %" PRIu64
-          " sec; timeout_per_batch: %" PRIu64 " sec; rss_limit_mb: %" PRIu64
-          " MB; stack_limit_kb: %" PRIu64 " KB\n",
-          state.run_time_flags.timeout_per_input.load(),
-          state.run_time_flags.timeout_per_batch,
+          "Starting watchdog thread: timeout_per_input_ms: %" PRIu64
+          "; timeout_per_batch_ms: %" PRIu64 "; rss_limit_mb: %" PRIu64
+          "; stack_limit_kb: %" PRIu64 "\n",
+          state.run_time_flags.timeout_per_input_ms.load(),
+          state.run_time_flags.timeout_per_batch_ms,
           state.run_time_flags.rss_limit_mb.load(),
           state.run_time_flags.stack_limit_kb.load());
   pthread_t watchdog_thread;
@@ -325,12 +325,12 @@
 }
 
 void GlobalRunnerState::ResetTimers() {
-  const auto curr_time = time(nullptr);
-  input_start_time = curr_time;
-  // batch_start_time is set only once -- just before the first input of the
+  const auto curr_time_ms = TimeInUsec() / 1000;
+  input_start_time_ms = curr_time_ms;
+  // batch_start_time_ms is set only once -- just before the first input of the
   // batch is about to start running.
-  if (batch_start_time == 0) {
-    batch_start_time = curr_time;
+  if (batch_start_time_ms == 0) {
+    batch_start_time_ms = curr_time_ms;
   }
 }
 
@@ -627,7 +627,7 @@
   int target_return_value = callbacks.Execute({data, size}) ? 0 : -1;
   state.stats.exec_time_usec = UsecSinceLast();
   CheckWatchdogLimits();
-  if (fuzztest::internal::state.input_start_time.exchange(0) != 0) {
+  if (fuzztest::internal::state.input_start_time_ms.exchange(0) != 0) {
     PostProcessCoverage(target_return_value);
   }
   state.stats.post_time_usec = UsecSinceLast();
@@ -1207,13 +1207,14 @@
   fuzztest::internal::state.run_time_flags.stack_limit_kb = stack_limit_kb;
 }
 
-extern "C" void CentipedeSetTimeoutPerInput(uint64_t timeout_per_input) {
-  fprintf(stderr,
-          "CentipedeSetTimeoutPerInput: changing timeout_per_input to %" PRIu64
-          "\n",
-          timeout_per_input);
-  fuzztest::internal::state.run_time_flags.timeout_per_input =
-      timeout_per_input;
+extern "C" void CentipedeSetTimeoutPerInput(uint64_t timeout_per_input_ms) {
+  fprintf(
+      stderr,
+      "CentipedeSetTimeoutPerInput: changing timeout_per_input_ms to %" PRIu64
+      "\n",
+      timeout_per_input_ms);
+  fuzztest::internal::state.run_time_flags.timeout_per_input_ms =
+      timeout_per_input_ms;
 }
 
 extern "C" __attribute__((weak)) const char *absl_nullable
@@ -1244,8 +1245,8 @@
     _exit(EXIT_FAILURE);
   }
   in_execution_batch = false;
-  fuzztest::internal::state.input_start_time = 0;
-  fuzztest::internal::state.batch_start_time = 0;
+  fuzztest::internal::state.input_start_time_ms = 0;
+  fuzztest::internal::state.batch_start_time_ms = 0;
 }
 
 extern "C" void CentipedePrepareProcessing() {
@@ -1255,7 +1256,7 @@
 
 extern "C" void CentipedeFinalizeProcessing() {
   fuzztest::internal::CheckWatchdogLimits();
-  if (fuzztest::internal::state.input_start_time.exchange(0) != 0) {
+  if (fuzztest::internal::state.input_start_time_ms.exchange(0) != 0) {
     fuzztest::internal::PostProcessCoverage(/*target_return_value=*/0);
   }
 }
diff --git a/centipede/runner.h b/centipede/runner.h
index 8e4ff8e..089068d 100644
--- a/centipede/runner.h
+++ b/centipede/runner.h
@@ -64,8 +64,8 @@
   uint64_t callstack_level : 8;
   uint64_t use_counter_features : 1;
   uint64_t use_auto_dictionary : 1;
-  std::atomic<uint64_t> timeout_per_input;
-  uint64_t timeout_per_batch;
+  std::atomic<uint64_t> timeout_per_input_ms;
+  uint64_t timeout_per_batch_ms;
   std::atomic<uint64_t> stack_limit_kb;
   std::atomic<uint64_t> rss_limit_mb;
   uint64_t crossover_level;
@@ -171,8 +171,8 @@
       /*callstack_level=*/HasIntFlag(":callstack_level=", 0),
       /*use_counter_features=*/HasFlag(":use_counter_features:"),
       /*use_auto_dictionary=*/HasFlag(":use_auto_dictionary:"),
-      /*timeout_per_input=*/HasIntFlag(":timeout_per_input=", 0),
-      /*timeout_per_batch=*/HasIntFlag(":timeout_per_batch=", 0),
+      /*timeout_per_input_ms=*/HasIntFlag(":timeout_per_input_ms=", 0),
+      /*timeout_per_batch_ms=*/HasIntFlag(":timeout_per_batch_ms=", 0),
       /*stack_limit_kb=*/HasIntFlag(":stack_limit_kb=", 0),
       /*rss_limit_mb=*/HasIntFlag(":rss_limit_mb=", 0),
       /*crossover_level=*/HasIntFlag(":crossover_level=", 50),
@@ -339,10 +339,10 @@
 
   // Per-input timer. Initially, zero. ResetInputTimer() sets it to the current
   // time.
-  std::atomic<time_t> input_start_time;
+  std::atomic<time_t> input_start_time_ms;
   // Per-batch timer. Initially, zero. ResetInputTimer() sets it to the current
   // time before the first input and never resets it.
-  std::atomic<time_t> batch_start_time;
+  std::atomic<time_t> batch_start_time_ms;
 
   // The Watchdog thread sets this to true.
   std::atomic<bool> watchdog_thread_started;
diff --git a/centipede/runner_interface.h b/centipede/runner_interface.h
index f12691d..5b6fe1e 100644
--- a/centipede/runner_interface.h
+++ b/centipede/runner_interface.h
@@ -72,8 +72,8 @@
 // Reconfigures the stack limit to `stack_limit_kb` - 0 indicates no limit.
 extern "C" void CentipedeSetStackLimit(size_t stack_limit_kb);
 
-// Reconfigures `timeout_per_input` accordingly in seconds - 0 means no timeout.
-extern "C" void CentipedeSetTimeoutPerInput(uint64_t timeout_per_input);
+// Reconfigures input timeout to `timeout_per_input_ms` - 0 means no timeout.
+extern "C" void CentipedeSetTimeoutPerInput(uint64_t timeout_per_input_ms);
 
 // An overridable function to get the runner flags for configuring the runner
 // during the initialization. The default implementation (as a weak function)
diff --git a/centipede/testing/runner_test.sh b/centipede/testing/runner_test.sh
index c98acc2..35de1a1 100755
--- a/centipede/testing/runner_test.sh
+++ b/centipede/testing/runner_test.sh
@@ -106,14 +106,14 @@
 CENTIPEDE_RUNNER_FLAGS=":rss_limit_mb=8192:" $target "${oom}"  # must pass
 
 echo ======== Check timeout
-CENTIPEDE_RUNNER_FLAGS=":timeout_per_input=567:" "${target}" \
-  2>&1 | grep "timeout_per_input: 567"
+CENTIPEDE_RUNNER_FLAGS=":timeout_per_input_ms=567000:" "${target}" \
+  2>&1 | grep "timeout_per_input_ms: 567"
 
-CENTIPEDE_RUNNER_FLAGS=":timeout_per_input=2:" "${target}" "${slo}" \
+CENTIPEDE_RUNNER_FLAGS=":timeout_per_input_ms=2000:" "${target}" "${slo}" \
   2>&1 | grep "Per-input timeout exceeded"
 
 {
-    CENTIPEDE_RUNNER_FLAGS=":ignore_timeout_reports:timeout_per_input=2:" "${target}" "${slo}";
+    CENTIPEDE_RUNNER_FLAGS=":ignore_timeout_reports:timeout_per_input_ms=2000:" "${target}" "${slo}";
     echo "$?" > "${TEST_TMPDIR}/ignore_timeout_reports_exit_code";
 } 2>&1 | grep "Per-input timeout exceeded" | grep "exiting without reporting as an error"
 ((`cat "${TEST_TMPDIR}/ignore_timeout_reports_exit_code"` == 0))
diff --git a/fuzztest/internal/centipede_adaptor.cc b/fuzztest/internal/centipede_adaptor.cc
index 7eb0e87..54290ee 100644
--- a/fuzztest/internal/centipede_adaptor.cc
+++ b/fuzztest/internal/centipede_adaptor.cc
@@ -583,7 +583,8 @@
     absl::FPrintF(GetStderr(),
                   "[.] Per-input time limit set to: %" PRId64 "s\n",
                   time_limit_seconds);
-    CentipedeSetTimeoutPerInput(time_limit_seconds);
+    CentipedeSetTimeoutPerInput(/*timeout_per_input_ms=*/time_limit_seconds *
+                                1000);
   }
 }