diff --git a/examples/runner/main.rs b/examples/runner/main.rs
index 60e10ba..106be5d 100644
--- a/examples/runner/main.rs
+++ b/examples/runner/main.rs
@@ -1,12 +1,22 @@
-use ixa::runner::run_with_args;
+use clap::Args;
+use ixa::runner::run_with_custom_args;
+
+#[derive(Args, Debug)]
+struct Extra {
+    #[arg(short, long)]
+    foo: bool,
+}
 
 fn main() {
     // Try running this with `cargo run --example runner -- --seed 42`
-    run_with_args(|context, args| {
+    run_with_custom_args(|context, args, extra: Option<Extra>| {
         context.add_plan(1.0, |_| {
             println!("Hello, world!");
         });
         println!("{}", args.seed);
+        if let Some(extra) = extra {
+            println!("{}", extra.foo);
+        }
         Ok(())
     })
     .unwrap();
diff --git a/src/runner.rs b/src/runner.rs
index 37cff45..6795e89 100644
--- a/src/runner.rs
+++ b/src/runner.rs
@@ -5,11 +5,10 @@ use crate::error::IxaError;
 use crate::global_properties::ContextGlobalPropertiesExt;
 use crate::random::ContextRandomExt;
 use crate::report::ContextReportExt;
-use clap::Parser;
+use clap::{Args, Command, FromArgMatches as _};
 
-#[derive(Parser, Debug)]
-#[command(version, about, long_about = None)]
-pub struct Args {
+#[derive(Args, Debug)]
+pub struct BaseArgs {
     /// Random seed
     #[arg(short, long, default_value = "0")]
     pub seed: u64,
@@ -23,18 +22,41 @@ pub struct Args {
     pub output_dir: String,
 }
 
+#[derive(Args)]
+pub struct PlaceholderCustom {}
+
 #[allow(clippy::missing_errors_doc)]
-pub fn run_with_args<F>(load: F) -> Result<(), Box<dyn std::error::Error>>
+pub fn run_with_custom_args<A, F>(load: F) -> Result<(), Box<dyn std::error::Error>>
 where
-    F: Fn(&mut Context, Args) -> Result<(), IxaError>,
+    A: Args,
+    F: Fn(&mut Context, BaseArgs, Option<A>) -> Result<(), IxaError>,
 {
-    run_with_args_internal(Args::parse(), load)
+    let cli = Command::new("Ixa");
+    let cli = BaseArgs::augment_args(cli);
+    let cli = A::augment_args(cli);
+    let matches = cli.get_matches();
+
+    let base_args_matches = BaseArgs::from_arg_matches(&matches)?;
+    let custom_matches = A::from_arg_matches(&matches)?;
+
+    run_with_args_internal(base_args_matches, Some(custom_matches), load)
 }
 
-fn run_with_args_internal<F>(args: Args, load: F) -> Result<(), Box<dyn std::error::Error>>
+#[allow(clippy::missing_errors_doc)]
+pub fn run_with_args<F>(load: F) -> Result<(), Box<dyn std::error::Error>>
 where
-    F: Fn(&mut Context, Args) -> Result<(), IxaError>,
+    F: Fn(&mut Context, BaseArgs, Option<PlaceholderCustom>) -> Result<(), IxaError>,
 {
+    let cli = Command::new("Ixa");
+    let cli = BaseArgs::augment_args(cli);
+    let matches = cli.get_matches();
+
+    let base_args_matches = BaseArgs::from_arg_matches(&matches)?;
+
+    run_with_args_internal(base_args_matches, None, load)
+}
+
+fn setup_context(args: &BaseArgs) -> Result<Context, IxaError> {
     // Instantiate a context
     let mut context = Context::new();
 
@@ -53,9 +75,23 @@ where
     }
 
     context.init_random(args.seed);
+    Ok(context)
+}
+
+fn run_with_args_internal<A, F>(
+    args: BaseArgs,
+    custom_args: Option<A>,
+    load: F,
+) -> Result<(), Box<dyn std::error::Error>>
+where
+    A: Args,
+    F: Fn(&mut Context, BaseArgs, Option<A>) -> Result<(), IxaError>,
+{
+    // Create a context
+    let mut context = setup_context(&args)?;
 
     // Run the provided Fn
-    load(&mut context, args)?;
+    load(&mut context, args, custom_args)?;
 
     // Execute the context
     context.execute();
@@ -68,20 +104,32 @@ mod tests {
     use crate::define_global_property;
     use serde::Deserialize;
 
+    #[derive(Args, Debug)]
+    struct CustomArgs {
+        #[arg(short, long, default_value = "0")]
+        field: u32,
+    }
+
+    #[test]
+    fn test_run_with_custom_args() {
+        let result = run_with_custom_args(|_, _, _: Option<CustomArgs>| Ok(()));
+        assert!(result.is_ok());
+    }
+
     #[test]
-    fn test_run_with_args_default() {
-        let result = run_with_args(|_, _| Ok(()));
+    fn test_run_with_args() {
+        let result = run_with_args(|_, _, _| Ok(()));
         assert!(result.is_ok());
     }
 
     #[test]
     fn test_run_with_random_seed() {
-        let test_args = Args {
+        let test_args = BaseArgs {
             seed: 42,
             config: String::new(),
             output_dir: String::new(),
         };
-        let result = run_with_args_internal(test_args, |ctx, _| {
+        let result = run_with_args_internal(test_args, None, |ctx, _, _: Option<CustomArgs>| {
             assert_eq!(ctx.get_base_seed(), 42);
             Ok(())
         });
@@ -96,12 +144,12 @@ mod tests {
 
     #[test]
     fn test_run_with_config_path() {
-        let test_args = Args {
+        let test_args = BaseArgs {
             seed: 42,
             config: "tests/data/global_properties_runner.json".to_string(),
             output_dir: String::new(),
         };
-        let result = run_with_args_internal(test_args, |ctx, _| {
+        let result = run_with_args_internal(test_args, None, |ctx, _, _: Option<CustomArgs>| {
             let p3 = ctx.get_global_property_value(RunnerProperty).unwrap();
             assert_eq!(p3.field_int, 0);
             Ok(())
@@ -111,12 +159,12 @@ mod tests {
 
     #[test]
     fn test_run_with_output_dir() {
-        let test_args = Args {
+        let test_args = BaseArgs {
             seed: 42,
             config: String::new(),
             output_dir: "data".to_string(),
         };
-        let result = run_with_args_internal(test_args, |ctx, _| {
+        let result = run_with_args_internal(test_args, None, |ctx, _, _: Option<CustomArgs>| {
             let output_dir = &ctx.report_options().directory;
             assert_eq!(output_dir, &PathBuf::from("data"));
             Ok(())