Is it possible to use fluent migrator in application_start?

PM> Install-Package FluentMigrator.Tools

Manually add a reference to:

packages\FluentMigrator.Tools.1.6.1\tools\AnyCPU\40\FluentMigrator.Runner.dll

Note that the folder name will vary on version number, this illustration uses the current 1.6.1 release. If you need the .NET 3.5 runner use the \35\ directory.

public static class Runner
{
    public class MigrationOptions : IMigrationProcessorOptions
    {
        public bool PreviewOnly { get; set; }
        public string ProviderSwitches { get; set; }
        public int Timeout { get; set; }
    }

    public static void MigrateToLatest(string connectionString)
    {
        // var announcer = new NullAnnouncer();
        var announcer = new TextWriterAnnouncer(s => System.Diagnostics.Debug.WriteLine(s));
        var assembly = Assembly.GetExecutingAssembly();

        var migrationContext = new RunnerContext(announcer)
        {
            Namespace = "MyApp.Sql.Migrations"
        };

        var options = new MigrationOptions { PreviewOnly=false, Timeout=60 };
        var factory = 
            new FluentMigrator.Runner.Processors.SqlServer.SqlServer2008ProcessorFactory();

        using (var processor = factory.Create(connectionString, announcer, options))
        { 
            var runner = new MigrationRunner(assembly, migrationContext, processor);
            runner.MigrateUp(true);
        }
    }
}

Note the SqlServer2008ProcessorFactory this is configurable dependent upon your database, there is support for: 2000, 2005, 2008, 2012, and 2014.