diff --git a/onnxruntime/test/perftest/README.md b/onnxruntime/test/perftest/README.md
index 59059cf6b62b7..4169d1bf54c65 100644
--- a/onnxruntime/test/perftest/README.md
+++ b/onnxruntime/test/perftest/README.md
@@ -35,6 +35,10 @@ Options:
 	-x: [intra_op_num_threads]: Sets the number of threads used to parallelize the execution within nodes. A value of 0 means the test will auto-select a default. Must >=0.
 	
 	-y: [inter_op_num_threads]: Sets the number of threads used to parallelize the execution of the graph (across nodes), A value of 0 means the test will auto-select a default. Must >=0.
+
+        -C: [session_config_entries]: Specify session configuration entries as key-value pairs: -C "<key1>|<val1> <key2>|<val2>"
+                                      Refer to onnxruntime_session_options_config_keys.h for valid keys and values.
+                                      [Example] -C "session.disable_cpu_ep_fallback|1 ep.context_enable|1"
 	
 	-h: help.
 
diff --git a/onnxruntime/test/perftest/command_args_parser.cc b/onnxruntime/test/perftest/command_args_parser.cc
index 6c1d447c7b3a3..7cfbe0a84e3e6 100644
--- a/onnxruntime/test/perftest/command_args_parser.cc
+++ b/onnxruntime/test/perftest/command_args_parser.cc
@@ -6,6 +6,9 @@
 
 #include <string.h>
 #include <iostream>
+#include <sstream>
+#include <string_view>
+#include <unordered_map>
 
 // Windows Specific
 #ifdef _WIN32
@@ -57,6 +60,9 @@ namespace perftest {
       "\t-d [CUDA only][cudnn_conv_algorithm]: Specify CUDNN convolution algorithms: 0(benchmark), 1(heuristic), 2(default). \n"
       "\t-q [CUDA only] use separate stream for copy. \n"
       "\t-z: Set denormal as zero. When turning on this option reduces latency dramatically, a model may have denormals.\n"
+      "\t-C: Specify session configuration entries as key-value pairs: -C \"<key1>|<value1> <key2>|<value2>\" \n"
+      "\t    Refer to onnxruntime_session_options_config_keys.h for valid keys and values. \n"
+      "\t    [Example] -C \"session.disable_cpu_ep_fallback|1 ep.context_enable|1\" \n"
       "\t-i: Specify EP specific runtime options as key value pairs. Different runtime options available are: \n"
       "\t    [DML only] [performance_preference]: DML device performance preference, options: 'default', 'minimum_power', 'high_performance', \n"
       "\t    [DML only] [device_filter]: DML device filter, options: 'any', 'gpu', 'npu', \n"
@@ -149,9 +155,42 @@ static bool ParseDimensionOverride(std::basic_string<ORTCHAR_T>& dim_identifier,
   return true;
 }
 
+static bool ParseSessionConfigs(const std::string& configs_string,
+                                std::unordered_map<std::string, std::string>& session_configs) {
+  std::istringstream ss(configs_string);
+  std::string token;
+
+  while (ss >> token) {
+    if (token == "") {
+      continue;
+    }
+
+    std::string_view token_sv(token);
+
+    auto pos = token_sv.find("|");
+    if (pos == std::string_view::npos || pos == 0 || pos == token_sv.length()) {
+      // Error: must use a '|' to separate the key and value for session configuration entries.
+      return false;
+    }
+
+    std::string key(token_sv.substr(0, pos));
+    std::string value(token_sv.substr(pos + 1));
+
+    auto it = session_configs.find(key);
+    if (it != session_configs.end()) {
+      // Error: specified duplicate session configuration entry: {key}
+      return false;
+    }
+
+    session_configs.insert(std::make_pair(std::move(key), std::move(value)));
+  }
+
+  return true;
+}
+
 /*static*/ bool CommandLineParser::ParseArguments(PerformanceTestConfig& test_config, int argc, ORTCHAR_T* argv[]) {
   int ch;
-  while ((ch = getopt(argc, argv, ORT_TSTR("b:m:e:r:t:p:x:y:c:d:o:u:i:f:F:S:T:AMPIDZvhsqz"))) != -1) {
+  while ((ch = getopt(argc, argv, ORT_TSTR("b:m:e:r:t:p:x:y:c:d:o:u:i:f:F:S:T:C:AMPIDZvhsqz"))) != -1) {
     switch (ch) {
       case 'f': {
         std::basic_string<ORTCHAR_T> dim_name;
@@ -322,6 +361,12 @@ static bool ParseDimensionOverride(std::basic_string<ORTCHAR_T>& dim_identifier,
       case 'T':
         test_config.run_config.intra_op_thread_affinities = ToUTF8String(optarg);
         break;
+      case 'C': {
+        if (!ParseSessionConfigs(ToUTF8String(optarg), test_config.run_config.session_config_entries)) {
+          return false;
+        }
+        break;
+      }
       case 'D':
         test_config.run_config.disable_spinning = true;
         break;
diff --git a/onnxruntime/test/perftest/ort_test_session.cc b/onnxruntime/test/perftest/ort_test_session.cc
index 6854a2649060a..87506c7240578 100644
--- a/onnxruntime/test/perftest/ort_test_session.cc
+++ b/onnxruntime/test/perftest/ort_test_session.cc
@@ -634,22 +634,41 @@ select from 'TF8', 'TF16', 'UINT8', 'FLOAT', 'ITENSOR'. \n)");
     session_options.DisableMemPattern();
   session_options.SetExecutionMode(performance_test_config.run_config.execution_mode);
 
+  // Set any extra session configuration entries provided by the user via command-line arguments.
+  //
+  // Some session config entries can also be set via dedicated command-line options.
+  // If the user uses multiple command-line options to set the same session config entry,
+  // we'll print a warning. Note that the dedicated command-line options will take precedence.
+  const auto& user_session_configs = performance_test_config.run_config.session_config_entries;
+  for (auto& it : user_session_configs) {
+    session_options.AddConfigEntry(it.first.c_str(), it.second.c_str());
+  }
+
+  auto warn_dup_config_entry = [&user_session_configs](const char* key) -> void {
+    if (user_session_configs.find(key) != user_session_configs.end()) {
+      fprintf(stderr, "[WARNING]: Trying to set session config entry '%s' via multiple command-line options\n", key);
+    }
+  };
+
   if (performance_test_config.run_config.intra_op_num_threads > 0) {
     fprintf(stdout, "Setting intra_op_num_threads to %d\n", performance_test_config.run_config.intra_op_num_threads);
     session_options.SetIntraOpNumThreads(performance_test_config.run_config.intra_op_num_threads);
   }
 
   if (!performance_test_config.run_config.intra_op_thread_affinities.empty()) {
+    warn_dup_config_entry(kOrtSessionOptionsConfigIntraOpThreadAffinities);
     fprintf(stdout, "Setting intra op thread affinity as %s\n", performance_test_config.run_config.intra_op_thread_affinities.c_str());
     session_options.AddConfigEntry(kOrtSessionOptionsConfigIntraOpThreadAffinities, performance_test_config.run_config.intra_op_thread_affinities.c_str());
   }
 
   if (performance_test_config.run_config.disable_spinning) {
+    warn_dup_config_entry(kOrtSessionOptionsConfigAllowIntraOpSpinning);
     fprintf(stdout, "Disabling intra-op thread spinning entirely\n");
     session_options.AddConfigEntry(kOrtSessionOptionsConfigAllowIntraOpSpinning, "0");
   }
 
   if (performance_test_config.run_config.disable_spinning_between_run) {
+    warn_dup_config_entry(kOrtSessionOptionsConfigForceSpinningStop);
     fprintf(stdout, "Disabling intra-op thread spinning between runs\n");
     session_options.AddConfigEntry(kOrtSessionOptionsConfigForceSpinningStop, "1");
   }
@@ -661,12 +680,16 @@ select from 'TF8', 'TF16', 'UINT8', 'FLOAT', 'ITENSOR'. \n)");
 
   // Set optimization level.
   session_options.SetGraphOptimizationLevel(performance_test_config.run_config.optimization_level);
-  if (!performance_test_config.run_config.profile_file.empty())
+  if (!performance_test_config.run_config.profile_file.empty()) {
     session_options.EnableProfiling(performance_test_config.run_config.profile_file.c_str());
-  if (!performance_test_config.run_config.optimized_model_path.empty())
+  }
+  if (!performance_test_config.run_config.optimized_model_path.empty()) {
     session_options.SetOptimizedModelFilePath(performance_test_config.run_config.optimized_model_path.c_str());
-  if (performance_test_config.run_config.set_denormal_as_zero)
+  }
+  if (performance_test_config.run_config.set_denormal_as_zero) {
+    warn_dup_config_entry(kOrtSessionOptionsConfigSetDenormalAsZero);
     session_options.AddConfigEntry(kOrtSessionOptionsConfigSetDenormalAsZero, "1");
+  }
   if (!performance_test_config.run_config.free_dim_name_overrides.empty()) {
     for (auto const& dim_override : performance_test_config.run_config.free_dim_name_overrides) {
       if (g_ort->AddFreeDimensionOverrideByName(session_options, ToUTF8String(dim_override.first).c_str(), dim_override.second) != nullptr) {
diff --git a/onnxruntime/test/perftest/test_configuration.h b/onnxruntime/test/perftest/test_configuration.h
index 43ad556247f97..5a49414a49004 100644
--- a/onnxruntime/test/perftest/test_configuration.h
+++ b/onnxruntime/test/perftest/test_configuration.h
@@ -6,6 +6,7 @@
 #include <map>
 #include <cstdint>
 #include <string>
+#include <unordered_map>
 
 #include "core/graph/constants.h"
 #include "core/framework/session_options.h"
@@ -56,6 +57,7 @@ struct RunConfig {
   bool do_cuda_copy_in_separate_stream{false};
   bool set_denormal_as_zero{false};
   std::basic_string<ORTCHAR_T> ep_runtime_config_string;
+  std::unordered_map<std::string, std::string> session_config_entries;
   std::map<std::basic_string<ORTCHAR_T>, int64_t> free_dim_name_overrides;
   std::map<std::basic_string<ORTCHAR_T>, int64_t> free_dim_denotation_overrides;
   std::string intra_op_thread_affinities;